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Crystal structure of rat methemoglobin in R2 state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DHT PDB ENTRY 3dht
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 50mM phosphate buffer, peg 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.14 α = 90 b = 54.015 β = 93.8 c = 115.008 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54170
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 30 97.4 0.1262 4.2 2.83 15682
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) 2.7 2.8 99.1 0.3198 1.2 2.68 1549
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 3dht 2.7 19.16 14091 1559 97.57 0.21906 0.21301 0.2127 0.27497 0.2723 RANDOM 23.491
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_3_deg 18.002 r_dihedral_angle_4_deg 6.43 r_dihedral_angle_1_deg 4.782 r_angle_refined_deg 1.028 r_scangle_it 0.648 r_mcangle_it 0.435 r_scbond_it 0.39 r_nbtor_refined 0.287 r_mcbond_it 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_3_deg 18.002 r_dihedral_angle_4_deg 6.43 r_dihedral_angle_1_deg 4.782 r_angle_refined_deg 1.028 r_scangle_it 0.648 r_mcangle_it 0.435 r_scbond_it 0.39 r_nbtor_refined 0.287 r_mcbond_it 0.239 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.188 r_chiral_restr 0.15 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.101 r_metal_ion_refined 0.025 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_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 4368 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 172
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement AUTOMAR data reduction