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Crystal structure of hemerythrin : L114Y mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 PEG 400, Ammonium acetate, Hepes
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.112 α = 90 b = 83.112 β = 90 c = 31.013 γ = 120
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 315r 2013-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1 NSRRC BL13C1
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 1.13 23.49 97.2 0.055 4.82 4.4 43683
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) 1 1.13 1.17 97.2 0.224 4.82 4.4 43683
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 2AVK 1.13 23.49 43683 2329 99.57 0.15045 0.14944 0.1533 0.16971 0.1738 RANDOM 12.397
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 37.991 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_4_deg 7.246 r_long_range_B_refined 6.081 r_dihedral_angle_1_deg 5.488 r_scbond_it 2.839 r_angle_refined_deg 2.226 r_mcangle_it 1.337 r_mcbond_it 0.952 r_chiral_restr 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.991 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_4_deg 7.246 r_long_range_B_refined 6.081 r_dihedral_angle_1_deg 5.488 r_scbond_it 2.839 r_angle_refined_deg 2.226 r_mcangle_it 1.337 r_mcbond_it 0.952 r_chiral_restr 0.384 r_bond_refined_d 0.029 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing