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Crystal structure of a pyridoxamine 5'-phosphate oxidase-related protein (ssuidraft_2804) from streptococcus suis 89/1591 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4.5 277 40.0% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71 α = 90 b = 71 β = 90 c = 58.4 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2006-06-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97934, 0.97915 SSRL BL9-2
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 29.198 94.4 0.085 9.48 10580 40.243
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 2.07 81.4 0.726 1.9 1548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2 29.198 10536 503 99.5 0.193 0.19276 0.191 0.1984 0.231 0.2394 RANDOM 42.918
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] -1.21 -1.21 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_4_deg 23.648 r_dihedral_angle_3_deg 13.115 r_scangle_it 6.702 r_dihedral_angle_1_deg 6.344 r_scbond_it 5.491 r_mcangle_it 3.449 r_mcbond_it 2.361 r_angle_refined_deg 1.546 r_angle_other_deg 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_4_deg 23.648 r_dihedral_angle_3_deg 13.115 r_scangle_it 6.702 r_dihedral_angle_1_deg 6.344 r_scbond_it 5.491 r_mcangle_it 3.449 r_mcbond_it 2.361 r_angle_refined_deg 1.546 r_angle_other_deg 0.881 r_mcbond_other 0.509 r_symmetry_vdw_other 0.381 r_symmetry_vdw_refined 0.228 r_nbd_other 0.206 r_nbd_refined 0.198 r_nbtor_refined 0.193 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.14 r_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1101 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 10
Software Software Software Name Purpose MolProbity model building REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXE model building autoSHARP phasing