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Crystal structure of a putative metal-dependent hydrolase (yiza, bsu10800) from bacillus subtilis at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 NANODROP, 0.2M NaCl, 10.0% PEG 3000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.184 α = 90 b = 53.184 β = 90 c = 251.364 γ = 90
Symmetry Space Group P 41 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 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97925 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 29.761 100 0.094 0.094 5.4 6.7 29798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.92 0.92 0.8 6.9 2129
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.9 29.761 29655 1500 99.83 0.187 0.185 0.226 0.2844 RANDOM 27.46
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] -1.3 -1.3 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.149 r_dihedral_angle_4_deg 13.224 r_dihedral_angle_3_deg 10.904 r_scangle_it 5.67 r_scbond_it 4.402 r_dihedral_angle_1_deg 3.604 r_mcangle_it 2.608 r_mcbond_it 1.733 r_angle_refined_deg 1.429 r_angle_other_deg 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.149 r_dihedral_angle_4_deg 13.224 r_dihedral_angle_3_deg 10.904 r_scangle_it 5.67 r_scbond_it 4.402 r_dihedral_angle_1_deg 3.604 r_mcangle_it 2.608 r_mcbond_it 1.733 r_angle_refined_deg 1.429 r_angle_other_deg 1.31 r_mcbond_other 0.424 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.167 r_nbd_other 0.139 r_symmetry_vdw_other 0.118 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.075 r_nbtor_other 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2716 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing SHARP phasing