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Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (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 DL-malic acid pH 6.1, 13% PEG 3350 , VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.746 α = 90 b = 87.002 β = 90 c = 106.895 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 315r 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 37.29 100 0.096 0.096 18.3 7.2 28997 28997 15.9
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 2.11 99.8 0.38 0.38 5.7 7.2 4147
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 (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 37.29 27519 27519 1476 99.93 0.20408 0.20256 0.2037 0.2321 0.2351 RANDOM 14.231
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] -0.21 0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.301 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_4_deg 11.101 r_dihedral_angle_1_deg 4.856 r_scangle_it 1.076 r_angle_refined_deg 1.022 r_scbond_it 0.65 r_mcangle_it 0.432 r_nbtor_refined 0.292 r_mcbond_it 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.301 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_4_deg 11.101 r_dihedral_angle_1_deg 4.856 r_scangle_it 1.076 r_angle_refined_deg 1.022 r_scbond_it 0.65 r_mcangle_it 0.432 r_nbtor_refined 0.292 r_mcbond_it 0.259 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.091 r_symmetry_hbond_refined 0.066 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2827 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 28
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling