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Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 293 20 % PEG 6000, 1.0 M LiCl, 0.1 M MES, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.55 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.132 α = 90 b = 49.738 β = 123.73 c = 69.547 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 FLAT MIRROR 2002-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 25.29 95.4 0.083 10.4 3.5 17758 36.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 88 0.555 1.8 2.8
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 1FI2 1.95 25.29 16875 883 95.2 0.163 0.16 0.1729 0.217 0.2311 RANDOM 32.48
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] 1.9 1.66 -0.05 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_4_deg 11.733 r_dihedral_angle_1_deg 6.172 r_scangle_it 4.474 r_scbond_it 2.675 r_angle_refined_deg 1.568 r_mcangle_it 1.483 r_angle_other_deg 0.849 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_4_deg 11.733 r_dihedral_angle_1_deg 6.172 r_scangle_it 4.474 r_scbond_it 2.675 r_angle_refined_deg 1.568 r_mcangle_it 1.483 r_angle_other_deg 0.849 r_mcbond_it 0.802 r_symmetry_hbond_refined 0.269 r_symmetry_vdw_other 0.239 r_xyhbond_nbd_refined 0.207 r_nbd_refined 0.19 r_nbd_other 0.187 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.097 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_bond_other_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1772 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 14
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling