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Crystal structure of conserved uncharacterized protein from Rhodopirellula baltica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NR4 PDB entry 2NR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 294 100mM Bis-tris pH 5.5, 25% PEG 3350, 200mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.268 α = 93.89 b = 58.315 β = 91.12 c = 73.799 γ = 90.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MAR CCD 165 mm 2006-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 1.21 50 92.7 0.063 0.051 6.6 3.8 231519 11.74
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 1.21 1.25 79.5 0.58 0.6 1.3 3.2
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 PDB entry 2NR4 1.21 20 224617 6990 93.61 0.17713 0.17636 0.175 0.20237 0.201 RANDOM 21.252
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] -0.61 -0.15 -0.13 0.31 -0.11 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.827 r_dihedral_angle_4_deg 15.139 r_dihedral_angle_3_deg 12.415 r_scangle_it 9.111 r_dihedral_angle_1_deg 5.779 r_scbond_it 5.691 r_mcangle_it 3.857 r_mcbond_it 2.337 r_angle_refined_deg 1.439 r_metal_ion_refined 0.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.827 r_dihedral_angle_4_deg 15.139 r_dihedral_angle_3_deg 12.415 r_scangle_it 9.111 r_dihedral_angle_1_deg 5.779 r_scbond_it 5.691 r_mcangle_it 3.857 r_mcbond_it 2.337 r_angle_refined_deg 1.439 r_metal_ion_refined 0.578 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.186 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 5976 Nucleic Acid Atoms Solvent Atoms 1341 Heterogen Atoms 20
Software Software Software Name Purpose PHASER phasing REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling