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Staphylopine dehydrogenase in complex with staphylopine and NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium acetate, 20-25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.18 α = 90 b = 49.14 β = 90 c = 58.71 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 100 PIXEL DECTRIS PILATUS3 2M 2017-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 93.59 99.4 10.8 4.2 118664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 99.6 2.2
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 6GMZ 2.21 93.59 26431 1438 99.42 0.22113 0.21761 0.2203 0.28848 0.2853 RANDOM 57.585
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] -4.99 -0.27 5.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_4_deg 18.947 r_dihedral_angle_3_deg 18.448 r_long_range_B_other 10.781 r_long_range_B_refined 10.771 r_scangle_other 8.115 r_dihedral_angle_1_deg 7.333 r_mcangle_it 6.424 r_mcangle_other 6.418 r_scbond_it 5.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_4_deg 18.947 r_dihedral_angle_3_deg 18.448 r_long_range_B_other 10.781 r_long_range_B_refined 10.771 r_scangle_other 8.115 r_dihedral_angle_1_deg 7.333 r_mcangle_it 6.424 r_mcangle_other 6.418 r_scbond_it 5.149 r_scbond_other 5.148 r_mcbond_it 4.307 r_mcbond_other 4.295 r_angle_refined_deg 1.829 r_angle_other_deg 1.024 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3476 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing