☰ Navigation Tabs
T-To-T(High) quaternary transitions in human hemoglobin: betaV33A oxy (2MM IHP, 20% PEG) (1 test set)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y22 PDB ENTRY 1Y22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2.
EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K.
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.6 α = 90 b = 99.2 β = 90 c = 66.6 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 169 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2001-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.5 33.3 94.8 0.108 5.9 3.1 21432
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) 2.5 2.7 89.7 0.294 2.4 2.8 4098
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 1Y22 2.5 10 17847 2021 88.8 0.19232 0.18435 0.1981 0.26377 0.2027 MATCHED TO PDB ENTRY 1Y22 43.841
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] 1.4 0.19 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.432 r_dihedral_angle_1_deg 4.008 r_scangle_it 3.604 r_scbond_it 2.198 r_angle_refined_deg 1.881 r_mcangle_it 1.627 r_angle_other_deg 1.232 r_mcbond_it 0.87 r_symmetry_hbond_refined 0.597 r_symmetry_vdw_refined 0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.432 r_dihedral_angle_1_deg 4.008 r_scangle_it 3.604 r_scbond_it 2.198 r_angle_refined_deg 1.881 r_mcangle_it 1.627 r_angle_other_deg 1.232 r_mcbond_it 0.87 r_symmetry_hbond_refined 0.597 r_symmetry_vdw_refined 0.455 r_nbd_refined 0.271 r_xyhbond_nbd_refined 0.248 r_nbd_other 0.226 r_symmetry_vdw_other 0.197 r_xyhbond_nbd_other 0.114 r_chiral_restr 0.102 r_bond_refined_d 0.024 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_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 4382 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 180
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling X-PLOR model building REFMAC refinement CCP4 data scaling X-PLOR phasing