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X-ray crystal structure of SRD42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 279 0.5 M Sodium chloride, 0.01 M Hexadecyltrimethylammonium bromide
Crystal Properties Matthews coefficient Solvent content 3.5 64.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.264 α = 90 b = 150.264 β = 90 c = 150.264 γ = 90
Symmetry Space Group P 43 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 81 PIXEL DECTRIS EIGER2 X 16M 2024-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.96860 CHESS 7B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 37.566 100 0.128 1 23.6 27.5 18413
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.609 100 1.408 0.699
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 2.6 37.566 17450 963 99.93 0.19856 0.19589 0.198 0.2469 0.2481 RANDOM 61.859
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.775 r_dihedral_angle_3_deg 14.554 r_mcangle_it 7.4 r_dihedral_angle_1_deg 6.939 r_scbond_it 5.854 r_mcbond_it 4.745 r_dihedral_angle_2_deg 4.623 r_angle_refined_deg 1.459 r_chiral_restr 0.113 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.775 r_dihedral_angle_3_deg 14.554 r_mcangle_it 7.4 r_dihedral_angle_1_deg 6.939 r_scbond_it 5.854 r_mcbond_it 4.745 r_dihedral_angle_2_deg 4.623 r_angle_refined_deg 1.459 r_chiral_restr 0.113 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2827 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing