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CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.95 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R3B PDB entry 2R3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 NANODROP, 10.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.888 α = 90 b = 109.888 β = 90 c = 54.193 γ = 90
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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.00000 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 27.472 99.9 0.063 0.063 6.2 5.4 23697 37.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.666 0.666 1.1 5.4 1758
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2R3B 1.95 27.472 23697 1216 99.84 0.157 0.157 0.155 0.194 0.2491 RANDOM 37.69
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] -0.74 -0.74 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.998 r_dihedral_angle_3_deg 14.108 r_dihedral_angle_4_deg 11.811 r_scangle_it 6.879 r_dihedral_angle_1_deg 5.969 r_scbond_it 5.451 r_mcangle_it 2.971 r_mcbond_it 2.189 r_angle_refined_deg 1.427 r_angle_other_deg 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.998 r_dihedral_angle_3_deg 14.108 r_dihedral_angle_4_deg 11.811 r_scangle_it 6.879 r_dihedral_angle_1_deg 5.969 r_scbond_it 5.451 r_mcangle_it 2.971 r_mcbond_it 2.189 r_angle_refined_deg 1.427 r_angle_other_deg 0.927 r_mcbond_other 0.52 r_symmetry_vdw_other 0.243 r_nbd_refined 0.218 r_nbd_other 0.184 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.103 r_nbtor_other 0.088 r_chiral_restr 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction MOLREP phasing