☰ Navigation Tabs
Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 12.0% PEG-20000, 0.1M MES pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.688 α = 90 b = 85.55 β = 130.2 c = 48.725 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 2004-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 1.9 99 99.47 0.066 28.05 4.81 17410 55.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 95.32 1.34 3.41 836
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 1EIX 2 27 14180 758 99.61 0.18343 0.18139 0.1885 0.22088 0.2304 RANDOM 58.589
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] 2.07 -1.36 -3.3 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_3_deg 14.754 r_dihedral_angle_1_deg 6.244 r_scangle_it 3.323 r_scbond_it 2.256 r_angle_refined_deg 1.671 r_mcangle_it 1.476 r_mcbond_it 0.995 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_3_deg 14.754 r_dihedral_angle_1_deg 6.244 r_scangle_it 3.323 r_scbond_it 2.256 r_angle_refined_deg 1.671 r_mcangle_it 1.476 r_mcbond_it 0.995 r_angle_other_deg 0.839 r_symmetry_vdw_refined 0.494 r_mcbond_other 0.257 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.213 r_nbtor_refined 0.185 r_nbd_other 0.183 r_symmetry_vdw_other 0.178 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.103 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1457 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement