1RQ3

Crystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Deoxyhemoglobin, Deoxyhemoglobin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HBB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5651.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97α = 90
b = 99.3β = 90
c = 66γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMS1990-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9195.30.0423.23.947999
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.912.0578.10.1052.92.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1HBB1.91104314943149483294.110.167270.19838RANDOM23.779
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]
-0.431.59-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.789
r_scangle_it5.074
r_dihedral_angle_1_deg3.831
r_scbond_it3.159
r_mcangle_it2.064
r_angle_refined_deg1.86
r_mcbond_it1.072
r_angle_other_deg0.824
r_symmetry_vdw_other0.328
r_nbd_refined0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.789
r_scangle_it5.074
r_dihedral_angle_1_deg3.831
r_scbond_it3.159
r_mcangle_it2.064
r_angle_refined_deg1.86
r_mcbond_it1.072
r_angle_other_deg0.824
r_symmetry_vdw_other0.328
r_nbd_refined0.236
r_symmetry_vdw_refined0.232
r_nbd_other0.186
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.147
r_chiral_restr0.114
r_xyhbond_nbd_other0.091
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.001
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4384
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing