2D5Z | pdb_00002d5z

Crystal structure of T-state human hemoglobin complexed with three L35 molecules

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	5.8	293	18% PEG 6000, 100mM Na-Cacodylate, 0.1mM L35, pH 5.8, BATCH, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.028	α = 90
b = 82.697	β = 90
c = 110.343	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

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	1.45	20	88.8	0.038	15.8	2.88		91355

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)
	1.45	1.5	54.9		0.181

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.45	19.65	86684	4573	100	0.18732	0.18585	0.19	0.21516	0.21	RANDOM	19.331

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]
-0.28			-0.5		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.674
r_dihedral_angle_3_deg	12.658
r_dihedral_angle_4_deg	10.983
r_dihedral_angle_1_deg	4.692
r_scangle_it	2.701
r_scbond_it	1.727
r_angle_refined_deg	1.363
r_mcangle_it	1.079
r_mcbond_it	0.693
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.674
r_dihedral_angle_3_deg	12.658
r_dihedral_angle_4_deg	10.983
r_dihedral_angle_1_deg	4.692
r_scangle_it	2.701
r_scbond_it	1.727
r_angle_refined_deg	1.363
r_mcangle_it	1.079
r_mcbond_it	0.693
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4370
Nucleic Acid Atoms
Solvent Atoms	614
Heterogen Atoms	247

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.