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Crystal structure of Canton G6PD in complex with structural NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M AMMONIUM CITRATE TRIBASIC 20%
W/V PEG 3350 0.5 MM AG1, PH 7.0, VAPOR DIFFUSION, SITTING DROP,
TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.12 α = 90 b = 206.25 β = 90 c = 211.84 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 PILATUS 6M 2015-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.6 50.01 100 0.153 10.5 7.3 171050
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 2.6 2.74 100 1.445 1.5 7.5
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 (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 5VFL 2.6 50.01 162393 8556 99.96 0.1885 0.18732 0.1935 0.21132 0.2162 RANDOM 59.785
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] -0.74 0.88 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.671 r_dihedral_angle_4_deg 19.774 r_dihedral_angle_3_deg 16.205 r_dihedral_angle_1_deg 6.296 r_long_range_B_refined 5.562 r_long_range_B_other 5.56 r_scangle_other 3.726 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scbond_it 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.671 r_dihedral_angle_4_deg 19.774 r_dihedral_angle_3_deg 16.205 r_dihedral_angle_1_deg 6.296 r_long_range_B_refined 5.562 r_long_range_B_other 5.56 r_scangle_other 3.726 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scbond_it 2.32 r_scbond_other 2.32 r_mcbond_it 1.845 r_mcbond_other 1.844 r_angle_refined_deg 1.734 r_angle_other_deg 0.882 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 31554 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 598
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement