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Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% w/v 1,6-Hexanediol, 0.2M MgCl2 and 20% w/v Polyethylene glycol 3350
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.396 α = 90 b = 68.17 β = 106.31 c = 63.93 γ = 90
Symmetry Space Group C 1 2 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 Mirrors 2010-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9795 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 2.19 50 99.5 0.101 21.4 7.1 27429 27429
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 2.19 2.27 98.9 0.122 6.8 2716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.19 50 26005 26005 1360 98.43 0.20726 0.20487 0.2053 0.25186 0.2102 RANDOM 17.602
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] -0.86 -0.54 0.26 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.077 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.47 r_scbond_it 2.207 r_angle_refined_deg 1.345 r_mcangle_it 1.175 r_mcbond_it 0.604 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.077 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.47 r_scbond_it 2.207 r_angle_refined_deg 1.345 r_mcangle_it 1.175 r_mcbond_it 0.604 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3461 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms
Software Software Software Name Purpose CBASS data collection SHELX model building REFMAC refinement DENZO data reduction HKL-2000 data scaling SHELX phasing