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Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme family protein from Roseovarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M NaCL, 0.1M HEPES pH 7.5, 1.6M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.594 α = 90 b = 91.362 β = 90 c = 100.271 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 315 mirrors 2011-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08 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 1.97 50 99.9 0.059 12.5 12.9 71641 71641
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 1.97 2.04 100 0.233 5 12.6 7073
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 3T8Q 1.97 46.99 71641 67733 3617 99.58 0.1826 0.18066 0.1874 0.21907 0.2247 RANDOM 21.53
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] -0.03 0.07 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 13.731 r_dihedral_angle_1_deg 6.98 r_scangle_it 5.853 r_scbond_it 3.852 r_mcangle_it 2.31 r_angle_refined_deg 2.179 r_mcbond_it 1.465 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 13.731 r_dihedral_angle_1_deg 6.98 r_scangle_it 5.853 r_scbond_it 3.852 r_mcangle_it 2.31 r_angle_refined_deg 2.179 r_mcbond_it 1.465 r_chiral_restr 0.178 r_bond_refined_d 0.031 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5679 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 32
Software Software Software Name Purpose CBASS data collection MOLREP phasing CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing