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PF1283- Rubrerythrin from Pyrococcus furiosus iron bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NNQ PDB ENTRY 1NNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 291 20% (w/v) PEG-3000,0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.85 56.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.402 α = 90 b = 105.402 β = 90 c = 80.095 γ = 90
Symmetry Space Group P 42 21 2
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 300 mm CCD ROSENBAUM 2006-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.7 19.73 100 0.096 12.8 13.9 12220 2
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 2.7 2.77 100 0.268 26.1 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER THROUGHOUT PDB ENTRY 1NNQ 2.7 19.71 12220 12220 624 100 0.18 0.176 0.1706 0.247 RANDOM 23.09
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.413 r_dihedral_angle_4_deg 29.607 r_dihedral_angle_3_deg 18.282 r_scangle_it 6.693 r_dihedral_angle_1_deg 6.324 r_scbond_it 4.473 r_mcbond_it 2.333 r_angle_refined_deg 2.181 r_mcangle_it 2.021 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.413 r_dihedral_angle_4_deg 29.607 r_dihedral_angle_3_deg 18.282 r_scangle_it 6.693 r_dihedral_angle_1_deg 6.324 r_scbond_it 4.473 r_mcbond_it 2.333 r_angle_refined_deg 2.181 r_mcangle_it 2.021 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.142 r_bond_refined_d 0.029 r_gen_planes_refined 0.009 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_refined 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 2726 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 6
Software Software Software Name Purpose CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing