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T-To-T(High) quaternary transitions in human hemoglobin: alphaY140F oxy (2MM IHP, 20% PEG) (1 test set)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y0C PDB ENTRY 1Y0C
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 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.6 α = 90 b = 98.6 β = 90 c = 67.1 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 2001-05-21 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 3.3 34.3 92.3 0.114 5.8 2.8 9186
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) 3.3 3.56 85.9 0.241 2.8 2.7 1735
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1Y0C 3.3 10 2 7990 7968 712 92.3 0.127 0.1304 0.307 0.2738 MATCHED TO PDB ENTRY 1Y0C 20.66
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 31.6 p_staggered_tor 25.2 p_scangle_it 8.366 p_scbond_it 5.589 p_mcangle_it 3.559 p_planar_tor 2.6 p_mcbond_it 2.156 p_xyhbond_nbd 0.218 p_multtor_nbd 0.208 p_singtor_nbd 0.179
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 31.6 p_staggered_tor 25.2 p_scangle_it 8.366 p_scbond_it 5.589 p_mcangle_it 3.559 p_planar_tor 2.6 p_mcbond_it 2.156 p_xyhbond_nbd 0.218 p_multtor_nbd 0.208 p_singtor_nbd 0.179 p_hb_or_metal_coord 0.17 p_chiral_restr 0.148 p_planar_d 0.043 p_angle_d 0.027 p_bond_d 0.01 p_plane_restr 0.01 p_angle_deg p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 180
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling X-PLOR model building PROLSQ refinement CCP4 data scaling X-PLOR phasing