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Crystal Structure of HbpS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Br phases
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 40% w/v PEG 400, 5% w/v PEG 3000, 100mM MES pH 5.8; Protein concentration of 14 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 37.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.522 α = 90 b = 152.522 β = 90 c = 152.522 γ = 90
Symmetry Space Group P 21 3
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 MAR CCD 165 mm 2007-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9778 EMBL/DESY, HAMBURG BW7A
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 2.2 20 98.5 0.073 12.63 4.18 60060 59161 -3 -3
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) 2.2 2.4 94.9 0.321 3.56 2.92 12979
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 SAD THROUGHOUT Br Phases 2.2 19.86 -3 -3 60060 55408 2915 99.08 0.20461 0.20461 0.20149 0.2953 0.26429 0.3348 RANDOM 67.795
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.754 r_dihedral_angle_1_deg 35.225 r_dihedral_angle_4_deg 23.164 r_dihedral_angle_3_deg 19.632 r_scangle_it 0.446 r_angle_refined_deg 0.358 r_nbtor_refined 0.302 r_mcangle_it 0.239 r_scbond_it 0.235 r_symmetry_hbond_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.754 r_dihedral_angle_1_deg 35.225 r_dihedral_angle_4_deg 23.164 r_dihedral_angle_3_deg 19.632 r_scangle_it 0.446 r_angle_refined_deg 0.358 r_nbtor_refined 0.302 r_mcangle_it 0.239 r_scbond_it 0.235 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.173 r_mcbond_it 0.131 r_chiral_restr 0.021 r_bond_refined_d 0.002 r_gen_planes_refined 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7976 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 8
Software Software Software Name Purpose MAR345 data collection SOLVE phasing REFMAC refinement XDS data reduction XSCALE data scaling