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Crystal structure of apo-CbbY from Rhodobacter sphaeroides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 16-20 % PEG-6000 and 0.1 M Hepes-NaOH pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.685 α = 90 b = 117.685 β = 90 c = 43.994 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97138 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 41.608 99.8 0.05 0.059 0.023 19.5 6.5 24048 24048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99 0.376 0.376 0.202 2 5.2 3458
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 SAD THROUGHOUT 1.9 20 23982 1199 100 0.2001 0.1989 0.2238 0.2175 RANDOM 28.125
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] -0.99 -0.99 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 18.207 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_1_deg 5.395 r_scangle_it 3.546 r_scbond_it 2.063 r_angle_refined_deg 1.232 r_mcangle_it 1.194 r_mcbond_it 0.619 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 18.207 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_1_deg 5.395 r_scangle_it 3.546 r_scbond_it 2.063 r_angle_refined_deg 1.232 r_mcangle_it 1.194 r_mcbond_it 0.619 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1724 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 6
Software Software Software Name Purpose SCALA data scaling RESOLVE model building PDB_EXTRACT data extraction REFMAC refinement XDS data reduction SCALA data scaling SHARP phasing XSCALE data reduction