1RPS | pdb_00001rps

Crystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Hemoglobin. Hemoglobin exposed to NO under anerobic conditions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RQ3	pdb id 1RQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	10 mg/mL human hemoglobin, 10 mM potassium phosphate, 100 mM potassium chloride, 10-12% PEG 6000, 3 mM sodium dithionite (under anaerobic conditions), BATCH METHOD, temperature 298K, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.56	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97	α = 90
b = 99.3	β = 90
c = 66.1	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	298	AREA DETECTOR	SDMS		1998-06-20	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	2.11	39.841	96.9	0.094	8.1	6.3	37996	37996

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)
	2.11	2.27	87.1		0.272	1.5	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 id 1RQ3	2.11	10	30288	30288	3440	89.73	0.18648	0.18136	0.19	0.23217	0.24	matched to that in PDB id 1RQ3	25.816

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]
-1.08			1.31		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.769
r_scangle_it	3.831
r_dihedral_angle_1_deg	3.651
r_scbond_it	2.34
r_angle_refined_deg	1.628
r_mcangle_it	1.526
r_mcbond_it	0.801
r_angle_other_deg	0.793
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.206
r_nbd_other	0.194
r_symmetry_vdw_other	0.175
r_symmetry_hbond_refined	0.122
r_xyhbond_nbd_other	0.111
r_chiral_restr	0.094
r_symmetry_vdw_refined	0.055
r_bond_refined_d	0.022
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	180

Software

Software
Software Name	Purpose
REFMAC	refinement
SDMS	data reduction
SDMS	data scaling
X-PLOR	phasing