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Imine reductase from Nocardiopsis halophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGY PDB ENTRY 3ZGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 18% (W/V) PEG 3350; 0. 2 M MGCL2; 0.1M BIS-TRIS PROPANE PH 5.5; 1% (W/V) N-OCTYL-BETA-D-OCTYLPYRANOSIDE
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.17 α = 90 b = 153.92 β = 90 c = 105.57 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PIXEL 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.39 67.57 99.8 0.07 15.1 6.8 94683 2
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 2.39 2.47 100 0.55 3.6 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ZGY 2.24 67.57 94683 5458 99.7 0.23199 0.2302 0.2352 0.26577 0.2692 RANDOM 48.319
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] -0.23 2.03 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.595 r_dihedral_angle_4_deg 22.986 r_dihedral_angle_3_deg 18.631 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.958 r_scbond_it 4.194 r_mcbond_it 4.053 r_mcbond_other 4.053 r_angle_other_deg 1.881 r_angle_refined_deg 1.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.595 r_dihedral_angle_4_deg 22.986 r_dihedral_angle_3_deg 18.631 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.958 r_scbond_it 4.194 r_mcbond_it 4.053 r_mcbond_other 4.053 r_angle_other_deg 1.881 r_angle_refined_deg 1.656 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 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 15838 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling MOLREP phasing