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Crystal structure of a putative racemase from Roseobacter denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 30% PEG MME 550, 0.1M HEPES, 0.05M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.492 α = 90 b = 64.745 β = 90 c = 76.449 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 MIRRORS 2011-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.88 50 97.1 0.069 23.4 12 73698 14.87
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) 1 1.88 1.91 66.4 0.259 4.7
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 3N4E 1.88 43.45 72505 72505 3703 97.2 0.195 0.195 0.1956 0.216 0.2159 RANDOM 17.8
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] -1.94 3.92 -1.97
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.731 c_scbond_it 1.851 c_mcangle_it 1.585 c_angle_deg 1.4 c_mcbond_it 1.09 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.731 c_scbond_it 1.851 c_mcangle_it 1.585 c_angle_deg 1.4 c_mcbond_it 1.09 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5806 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 54
Software Software Software Name Purpose CBASS data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling