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Crystal structure of a duf72 family protein (ef0366) from enterococcus faecalis v583 at 3.10 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPY pdb entry 1vpy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 6.5 277 1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.08 69.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.819 α = 90 b = 92.358 β = 90 c = 119.347 γ = 90
Symmetry Space Group P 21 21 21
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 (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) 2004-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 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 3.1 119.52 99.4 0.08 0.08 8.6 3.4 18876
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 3.1 3.27 99.7 0.392 0.392 1.9 3.5
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 MR THROUGHOUT pdb entry 1vpy 3.1 73.13 17862 975 100 0.193 0.19257 0.191 0.224 0.234 RANDOM 77.153
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] -0.99 -1.31 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 9.97 r_dihedral_angle_1_deg 4.42 r_scangle_it 3.46 r_scbond_it 2.268 r_mcangle_it 1.376 r_mcbond_it 0.809 r_angle_refined_deg 0.647 r_angle_other_deg 0.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_3_deg 11.289 r_dihedral_angle_4_deg 9.97 r_dihedral_angle_1_deg 4.42 r_scangle_it 3.46 r_scbond_it 2.268 r_mcangle_it 1.376 r_mcbond_it 0.809 r_angle_refined_deg 0.647 r_angle_other_deg 0.539 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.201 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.186 r_nbd_other 0.171 r_mcbond_other 0.147 r_symmetry_vdw_other 0.125 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.084 r_xyhbond_nbd_other 0.06 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4419 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction CCP4 data scaling PHASER phasing