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Carbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [450 min]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 1.87 34.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.373 α = 90 b = 30.592 β = 105.73 c = 63.814 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 140 CCD MAR CCD 165 mm 2008-02-21 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 80.5 0.054 8 3.2 31909 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.21 1.25 20.4 1.3 797
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 1MBC 1.21 16.54 31493 1564 80.56 0.166 0.163 0.1621 0.226 0.2263 RANDOM 16.759
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] 0.01 -0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.511 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 14.618 r_sphericity_free 13.947 r_scangle_it 8.664 r_sphericity_bonded 7.501 r_scbond_it 6.307 r_dihedral_angle_1_deg 5.58 r_mcangle_it 4.483 r_rigid_bond_restr 4.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.511 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 14.618 r_sphericity_free 13.947 r_scangle_it 8.664 r_sphericity_bonded 7.501 r_scbond_it 6.307 r_dihedral_angle_1_deg 5.58 r_mcangle_it 4.483 r_rigid_bond_restr 4.123 r_mcbond_it 3.372 r_angle_refined_deg 2.936 r_metal_ion_refined 0.454 r_nbtor_refined 0.333 r_nbd_refined 0.314 r_chiral_restr 0.226 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.153 r_bond_refined_d 0.036 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 140 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