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The Crystal Structure of MAPK2 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1M Sodium malonate dibasic monohydrate, 0.1M HEPES pH7, 0.5% v/v Jeffamine ED2003
Crystal Properties Matthews coefficient Solvent content 3.02 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.812 α = 90 b = 179.015 β = 90 c = 212.397 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953727 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.4 48.953 100 0.148 13 11.4 73900
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.47 1.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.4 48.953 73900 3807 99.947 0.216 0.2136 0.2147 0.2631 0.263 110.328
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 3.281 -3.018 -0.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.118 r_lrange_other 21.147 r_lrange_it 21.146 r_dihedral_angle_3_deg 14.434 r_scangle_it 13.713 r_scangle_other 13.713 r_mcangle_it 13.044 r_mcangle_other 13.044 r_dihedral_angle_4_deg 11.789 r_scbond_it 8.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.118 r_lrange_other 21.147 r_lrange_it 21.146 r_dihedral_angle_3_deg 14.434 r_scangle_it 13.713 r_scangle_other 13.713 r_mcangle_it 13.044 r_mcangle_other 13.044 r_dihedral_angle_4_deg 11.789 r_scbond_it 8.858 r_scbond_other 8.858 r_mcbond_it 8.469 r_mcbond_other 8.466 r_dihedral_angle_1_deg 5.876 r_angle_refined_deg 1.348 r_angle_other_deg 1.242 r_symmetry_nbd_refined 0.292 r_nbd_other 0.256 r_nbd_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.16 r_ncsr_local_group_59 0.124 r_ncsr_local_group_21 0.121 r_ncsr_local_group_66 0.121 r_ncsr_local_group_14 0.12 r_ncsr_local_group_19 0.12 r_ncsr_local_group_32 0.12 r_ncsr_local_group_60 0.12 r_ncsr_local_group_28 0.119 r_ncsr_local_group_39 0.119 r_ncsr_local_group_45 0.119 r_ncsr_local_group_54 0.119 r_ncsr_local_group_56 0.119 r_ncsr_local_group_5 0.118 r_ncsr_local_group_36 0.118 r_ncsr_local_group_38 0.118 r_ncsr_local_group_44 0.118 r_ncsr_local_group_51 0.118 r_ncsr_local_group_7 0.117 r_ncsr_local_group_11 0.117 r_ncsr_local_group_20 0.117 r_ncsr_local_group_23 0.117 r_ncsr_local_group_31 0.117 r_ncsr_local_group_40 0.117 r_ncsr_local_group_4 0.116 r_ncsr_local_group_9 0.116 r_ncsr_local_group_15 0.116 r_ncsr_local_group_43 0.116 r_xyhbond_nbd_refined 0.115 r_ncsr_local_group_24 0.115 r_ncsr_local_group_52 0.115 r_ncsr_local_group_65 0.115 r_ncsr_local_group_16 0.114 r_ncsr_local_group_25 0.113 r_ncsr_local_group_30 0.113 r_ncsr_local_group_33 0.113 r_ncsr_local_group_41 0.113 r_ncsr_local_group_50 0.113 r_ncsr_local_group_58 0.113 r_ncsr_local_group_29 0.112 r_ncsr_local_group_46 0.112 r_ncsr_local_group_47 0.112 r_ncsr_local_group_64 0.112 r_ncsr_local_group_17 0.111 r_ncsr_local_group_55 0.111 r_ncsr_local_group_3 0.11 r_ncsr_local_group_37 0.11 r_ncsr_local_group_63 0.109 r_ncsr_local_group_6 0.108 r_ncsr_local_group_10 0.108 r_ncsr_local_group_34 0.108 r_ncsr_local_group_49 0.108 r_ncsr_local_group_1 0.107 r_ncsr_local_group_26 0.107 r_ncsr_local_group_57 0.107 r_ncsr_local_group_53 0.106 r_ncsr_local_group_8 0.105 r_ncsr_local_group_13 0.105 r_ncsr_local_group_22 0.105 r_ncsr_local_group_62 0.105 r_ncsr_local_group_2 0.104 r_ncsr_local_group_42 0.104 r_ncsr_local_group_61 0.103 r_ncsr_local_group_12 0.101 r_ncsr_local_group_18 0.1 r_ncsr_local_group_27 0.1 r_ncsr_local_group_35 0.1 r_ncsr_local_group_48 0.1 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.063 r_xyhbond_nbd_other 0.032 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27342 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing