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Crystal structure of Corynebacterium glutamicum PimB' bound to GDP (orthorhombic crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKA PDB entry 3oka
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.1 291 0.1 M sodium citrate pH 5.1, 22% PEG 3350 , VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.852 α = 90 b = 86.4 β = 90 c = 106.639 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 ADSC QUANTUM 4 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.23 45.37 95.8 0.093 0.093 9.9 3.2 19982 19982 28
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) 2.23 2.35 72.5 0.382 0.382 2.3 2.3 4871
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3oka 2.4 45.36 15991 15991 851 99.69 0.19245 0.19245 0.19009 0.1913 0.23617 0.2368 RANDOM 20.345
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] -0.76 0.14 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 13.711 r_dihedral_angle_1_deg 4.957 r_scangle_it 1.472 r_angle_refined_deg 1.09 r_scbond_it 0.842 r_mcangle_it 0.547 r_mcbond_it 0.339 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 13.711 r_dihedral_angle_1_deg 4.957 r_scangle_it 1.472 r_angle_refined_deg 1.09 r_scbond_it 0.842 r_mcangle_it 0.547 r_mcbond_it 0.339 r_nbtor_refined 0.291 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.171 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.068 r_symmetry_hbond_refined 0.038 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2850 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 28
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling