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Crystal structure of unsaturated glucuronyl hydrolase from Streptcoccus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VD5 PDB ENTRY 1VD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.08 α = 90 b = 116.08 β = 90 c = 78.125 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD RIGAKU JUPITER 210 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.7 SPring-8 BL38B1
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 1.75 100 100 0.056 33.2 61457
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 1.75 1.81 100 0.38 3.89
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 MIR THROUGHOUT PDB ENTRY 1VD5 1.75 38 58318 3110 99.93 0.18308 0.18191 0.1807 0.20449 0.2035 RANDOM 21.133
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] 0.69 0.35 0.69 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 17.116 r_dihedral_angle_3_deg 11.747 r_dihedral_angle_1_deg 5.282 r_scangle_it 1.9 r_scbond_it 1.249 r_angle_refined_deg 1.001 r_mcangle_it 0.774 r_mcbond_it 0.457 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 17.116 r_dihedral_angle_3_deg 11.747 r_dihedral_angle_1_deg 5.282 r_scangle_it 1.9 r_scbond_it 1.249 r_angle_refined_deg 1.001 r_mcangle_it 0.774 r_mcbond_it 0.457 r_nbtor_refined 0.307 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.143 r_symmetry_hbond_refined 0.121 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3288 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing