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Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimental electron density from Selenium SAD experiment.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.75 291 26% Peg 4k, 0.1M Tris, 0.8M Lithium Chloride, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.12 60.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.112 α = 90 b = 118.112 β = 90 c = 65.792 γ = 120
Symmetry Space Group P 64 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 100 CCD MARRESEARCH 2004-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.98 NSLS X9A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 20 99.8 0.074 31.75 11.15 20050 20050
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.9 0.456 4.45 1998
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 SAD THROUGHOUT Experimental electron density from Selenium SAD experiment. 2.4 20 10470 529 99.59 0.23534 0.23244 0.2366 0.29466 0.2931 RANDOM 44.966
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] 2.58 1.29 2.58 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.527 r_scangle_it 7.926 r_scbond_it 5.288 r_mcangle_it 3.534 r_angle_refined_deg 3.232 r_mcbond_it 2.034 r_nbd_refined 0.312 r_metal_ion_refined 0.283 r_symmetry_vdw_refined 0.281 r_chiral_restr 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.527 r_scangle_it 7.926 r_scbond_it 5.288 r_mcangle_it 3.534 r_angle_refined_deg 3.232 r_mcbond_it 2.034 r_nbd_refined 0.312 r_metal_ion_refined 0.283 r_symmetry_vdw_refined 0.281 r_chiral_restr 0.238 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.187 r_bond_refined_d 0.046 r_gen_planes_refined 0.019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1262 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing