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The Crystal Structure of PTPRG from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M NaSCN, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.916 α = 90 b = 76.161 β = 90 c = 106.623 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 2020-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18064 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 2.55 47.27 100 0.162 9.3 7.2 20006
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 2.55 2.66 0.675
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.55 47.27 18972 988 99.94 0.2183 0.21522 0.2232 0.27749 0.2814 RANDOM 33.619
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] 1.69 -1.1 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.479 r_dihedral_angle_2_deg 6.003 r_long_range_B_refined 5.235 r_long_range_B_other 5.218 r_scangle_other 2.285 r_mcangle_it 2.117 r_mcangle_other 2.117 r_scbond_it 1.302 r_scbond_other 1.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.479 r_dihedral_angle_2_deg 6.003 r_long_range_B_refined 5.235 r_long_range_B_other 5.218 r_scangle_other 2.285 r_mcangle_it 2.117 r_mcangle_other 2.117 r_scbond_it 1.302 r_scbond_other 1.301 r_mcbond_it 1.209 r_mcbond_other 1.209 r_angle_refined_deg 1.015 r_angle_other_deg 0.344 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4620 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing