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Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-3) at 274K, Refmac5-refined
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 298 23% PEG 3350, 100MM TRIS-HCL PH 8.6,
200 MM MAGNESIUM CHLORIDE AND 2 MM DITHIOTHREITOL
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.31 α = 90 b = 58.215 β = 112.811 c = 69.03 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 274 PIXEL DECTRIS PILATUS 6M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.775 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.199 39.152 96.5 0.069 0.997 7.1 3.7 126107
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.199 1.22 91.9 1.737 0.309 1.1 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6NI6 1.199 39.152 126085 3768 96.351 0.125 0.1244 0.1243 0.151 0.1512 random 17.448
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] 0.134 0.215 -0.469 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.695 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_1_deg 6.025 r_lrange_it 3.142 r_lrange_other 2.863 r_scangle_it 2.636 r_scangle_other 2.636 r_scbond_it 2.104 r_scbond_other 2.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.695 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_1_deg 6.025 r_lrange_it 3.142 r_lrange_other 2.863 r_scangle_it 2.636 r_scangle_other 2.636 r_scbond_it 2.104 r_scbond_other 2.104 r_mcangle_other 1.745 r_mcangle_it 1.743 r_rigid_bond_restr 1.612 r_angle_refined_deg 1.529 r_angle_other_deg 1.489 r_mcbond_it 1.408 r_mcbond_other 1.399 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.185 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_other 0.177 r_symmetry_nbd_refined 0.165 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.145 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3368 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling PHASER phasing