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Crystal structure of mandelate racemase/muconate lactonizing enzyme from Jannaschia sp. CCS1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCY PDB ENTRY 3RCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 1.0 M Ammonium phosphate, 0.1 M citrate, pH 5.5, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.909 α = 90 b = 126.626 β = 90.08 c = 126.777 γ = 90
Symmetry Space Group P 1 21 1
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 2011-04-15 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 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 2.5 50 96.1 0.176 4.5 2.5 140837
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 2.5 2.54 96.9 0.984 2.4 7148
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3RCY 2.5 44.88 137531 6920 99.04 0.213 0.2112 0.177 0.2451 0.2011 RANDOM 29.8057
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] -7.73 3.5 0.23 7.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 17.62 r_dihedral_angle_1_deg 5.895 r_angle_refined_deg 1.185 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23476 Nucleic Acid Atoms Solvent Atoms 1201 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-3000 data reduction