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Crystal structure of human sepiapterin reductase in complex with an N-acetylserotinin analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2% W/V PEG1000, 2.5% V/V glycerol, 1.7 M Ammonium sulfate, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 4.58 73.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.84 α = 90 b = 144.84 β = 90 c = 180.695 γ = 120
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 2014-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.35 125.435 100 0.096 0.1 0.03 15.8 11.2 89220 89220 55.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 100 0.716 0.716 0.22 1 11.5 13018
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 FREE R-VALUE 4HWK 2.35 125.435 84419 4682 99.91 0.1868 0.1852 0.1933 0.2167 0.1917 RANDOM 48.374
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] 0.67 0.33 0.67 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.2 r_dihedral_angle_4_deg 22.307 r_dihedral_angle_3_deg 15.712 r_mcangle_it 6.449 r_dihedral_angle_1_deg 6.414 r_mcbond_it 4.664 r_mcbond_other 4.662 r_angle_refined_deg 1.219 r_angle_other_deg 0.658 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.2 r_dihedral_angle_4_deg 22.307 r_dihedral_angle_3_deg 15.712 r_mcangle_it 6.449 r_dihedral_angle_1_deg 6.414 r_mcbond_it 4.664 r_mcbond_other 4.662 r_angle_refined_deg 1.219 r_angle_other_deg 0.658 r_chiral_restr 0.065 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7744 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 313
Software Software Software Name Purpose PDB_EXTRACT data extraction REFMAC refinement Coot model building MOLREP phasing SCALA data scaling XDS data reduction