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Structure of trypsin solved by MR from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I8G PDB ENTRY 4I8G
Crystallization Crystal Properties Matthews coefficient Solvent content 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.835 α = 90 b = 64.682 β = 90 c = 69.96 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 PILATUS3 2M BE CRL 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 ESRF MASSIF-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 1.78 47.5 98.9 0.02 16.1 4.7 26622 3
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 1.78 1.85 93.1 1.47 1.6 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4I8G 1.78 47.49 25130 1450 98.68 0.18315 0.18165 0.21006 0.1984 RANDOM 33.826
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] 1.29 -1.3 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.583 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.531 r_scbond_it 2.249 r_mcangle_it 2.179 r_angle_refined_deg 1.893 r_mcbond_it 1.387 r_mcbond_other 1.377 r_angle_other_deg 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.583 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.531 r_scbond_it 2.249 r_mcangle_it 2.179 r_angle_refined_deg 1.893 r_mcbond_it 1.387 r_mcbond_other 1.377 r_angle_other_deg 1.02 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 1629 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing