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Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-2) at 274K, Refmac5-refined
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NI6 PDB entry 6NI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 298 23% PEG3350, 100 mM Tris-HCl, pH 8.6, 200 mM magnesium chloride, 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.297 α = 90 b = 58.215 β = 112.825 c = 69.052 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 1.2 38.672 97.4 0.068 0.998 6.8 2.7 127238
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 1.2 1.22 94.3 1.768 0.257 0.8 2.5
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 PDB entry 6NI6 1.2 38.672 127216 3838 97.25 0.124 0.1234 0.1231 0.1523 0.152 random 16.837
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] 0.04 -0.137 0.339 -0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.444 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_1_deg 6.043 r_lrange_it 3.119 r_lrange_other 2.85 r_scangle_it 2.614 r_scangle_other 2.614 r_scbond_it 2.136 r_scbond_other 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.444 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_1_deg 6.043 r_lrange_it 3.119 r_lrange_other 2.85 r_scangle_it 2.614 r_scangle_other 2.614 r_scbond_it 2.136 r_scbond_other 2.135 r_mcangle_other 1.729 r_mcangle_it 1.728 r_rigid_bond_restr 1.528 r_angle_refined_deg 1.52 r_angle_other_deg 1.486 r_mcbond_it 1.331 r_mcbond_other 1.323 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.175 r_symmetry_nbd_refined 0.172 r_nbd_other 0.166 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3368 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling PHASER phasing