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YpmB protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 10 mM nickel chloride, 25% PEG 2000 MME, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.2 α = 90 b = 52.415 β = 90 c = 55.079 γ = 90
Symmetry Space Group P 21 21 21
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 SBC-3 2006-04-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97872, 1.48520, 1.48590, 1.45180 APS 19-BM
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 1.74 28.3 98.4 0.056 25.5 4.7 12792 12792 30.7
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 1.74 1.78 88.6 0.451 2.44 3.5 790
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD 1.74 28.3 12750 12750 624 98.34 0.188 0.188 0.188 0.2144 0.1838 RANDOM 24.636
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] -1.29 0.76 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.228 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_1_deg 6.451 r_dihedral_angle_4_deg 5.325 r_scangle_it 4.261 r_scbond_it 2.869 r_mcangle_it 1.741 r_angle_refined_deg 1.576 r_mcbond_it 1.134 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.228 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_1_deg 6.451 r_dihedral_angle_4_deg 5.325 r_scangle_it 4.261 r_scbond_it 2.869 r_mcangle_it 1.741 r_angle_refined_deg 1.576 r_mcbond_it 1.134 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.136 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_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 1008 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection SCALEPACK data scaling HKL-3000 phasing SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing