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Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [450 min]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MBC PDB ENTRY 1MBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 6 293 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.446 α = 90 b = 30.721 β = 105.57 c = 63.891 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MAR CCD 165 mm 2007-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW14A 0.827 Photon Factory AR-NW14A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 98.2 0.049 11.7 3.6 38766 -3
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) 1.21 1.25 84.9 0.362 2.8 3281
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 1MBC 1.21 17.22 38747 1950 98.33 0.144 0.142 0.1408 0.183 0.1805 RANDOM 15.001
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] 0.02 -0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.685 r_dihedral_angle_4_deg 18.73 r_dihedral_angle_3_deg 14.204 r_sphericity_free 9.959 r_scangle_it 6.035 r_sphericity_bonded 5.677 r_dihedral_angle_1_deg 4.873 r_scbond_it 4.574 r_rigid_bond_restr 3.137 r_mcangle_it 3.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.685 r_dihedral_angle_4_deg 18.73 r_dihedral_angle_3_deg 14.204 r_sphericity_free 9.959 r_scangle_it 6.035 r_sphericity_bonded 5.677 r_dihedral_angle_1_deg 4.873 r_scbond_it 4.574 r_rigid_bond_restr 3.137 r_mcangle_it 3.079 r_mcbond_it 2.126 r_angle_refined_deg 1.863 r_metal_ion_refined 0.533 r_nbtor_refined 0.32 r_nbd_refined 0.307 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.134 r_xyhbond_nbd_refined 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling