☰ Navigation Tabs
Wild-Type Sperm Whale Myoglobin in Complex with Nitrosobenzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MBW PDB entry 2MBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 2.56 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA
Crystal Properties Matthews coefficient Solvent content 1.87 34.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.529 α = 90 b = 30.049 β = 104.55 c = 64.622 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 100 PIXEL DECTRIS PILATUS 300K 2014-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.75 50 99.7 0.036 0.9 29.1 3.1 13162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.347 0.9
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 2MBW 1.75 33.44 12365 590 98.11 0.23098 0.22875 0.2362 0.27612 0.2754 RANDOM 21.128
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] -0.2 0.05 0.16 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_4_deg 17.871 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 4.442 r_long_range_B_other 4.437 r_scangle_other 3.587 r_mcangle_it 2.389 r_mcangle_other 2.388 r_scbond_other 2.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_4_deg 17.871 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 4.442 r_long_range_B_other 4.437 r_scangle_other 3.587 r_mcangle_it 2.389 r_mcangle_other 2.388 r_scbond_other 2.311 r_scbond_it 2.308 r_mcbond_it 1.702 r_mcbond_other 1.674 r_angle_refined_deg 1.578 r_angle_other_deg 1.019 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1203 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing