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Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OLP PDB ENTRY 2OLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Capillary Counterdiffusion 5 293 Sodium Formate, pH 5.0, Capillary Counterdiffusion, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.973 α = 90 b = 73.973 β = 90 c = 153.194 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 ADSC QUANTUM 210 2007-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.88506 ESRF BM16
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 20 99.9 0.138 0.138 15.4 10.4 31837 31837 28.569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 100 0.422 9.5 3104
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OLP 1.95 20 1 31770 31770 1606 99.88 0.1767 0.1749 0.1753 0.2107 0.2113 RANDOM 32.0787
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 38.49 f_dihedral_angle_4_deg 25.403 f_dihedral_angle_3_deg 13.378 f_scangle_it 7.164 f_mcangle_it 5.285 f_scbond_it 5.149 f_dihedral_angle_1_deg 4.085 f_mcbond_it 3.693 f_angle_refined_deg 1.112 f_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 38.49 f_dihedral_angle_4_deg 25.403 f_dihedral_angle_3_deg 13.378 f_scangle_it 7.164 f_mcangle_it 5.285 f_scbond_it 5.149 f_dihedral_angle_1_deg 4.085 f_mcbond_it 3.693 f_angle_refined_deg 1.112 f_chiral_restr 0.07 f_bond_refined_d 0.01 f_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 90
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection