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Crystal structure of glycine oxidase from Geobacillus kaustophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYI PDB 1RYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 298 0.1 M phosphate-citrate buffer, 7% 2-propanol, 0.4 M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.89 57.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.945 α = 90 b = 87.945 β = 90 c = 413.456 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2014-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 98.6 0.096 0.098 0.022 11.5 20.6 48899 34.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.7 0.417 0.426 0.089 0.972 10.5 22.2 4774
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 1RYI 2.2 50 46153 2463 98.34 0.2345 0.2328 0.2334 0.2661 0.2637 RANDOM 44.542
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] 0.66 0.33 0.66 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.05 r_dihedral_angle_4_deg 19.13 r_dihedral_angle_3_deg 18.227 r_dihedral_angle_1_deg 5.804 r_scangle_it 1.885 r_angle_refined_deg 1.344 r_scbond_it 1.099 r_mcangle_it 0.804 r_mcbond_it 0.429 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.05 r_dihedral_angle_4_deg 19.13 r_dihedral_angle_3_deg 18.227 r_dihedral_angle_1_deg 5.804 r_scangle_it 1.885 r_angle_refined_deg 1.344 r_scbond_it 1.099 r_mcangle_it 0.804 r_mcbond_it 0.429 r_chiral_restr 0.101 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5510 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 136
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction