2DC3

Crystal structure of human cytoglobin at 1.68 angstroms resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.4M sodium acetate, 100mM sodium cacodylate, 5mM KCN, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.53	α = 90
b = 52.76	β = 87.75
c = 83.44	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	RIGAKU JUPITER 210		2004-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	1.000	SPring-8	BL45PX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.68	50	99.9	0.056	20.92	4.9	39043	39043			14.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.68	1.74	99.5		0.286	4.03	4.1	3849

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1V5H	1.68	20	37014	1927	99.8	0.142	0.14	0.181	RANDOM	14.13

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]
0.67		0.3	-0.23		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.06
r_dihedral_angle_4_deg	21.24
r_dihedral_angle_3_deg	13.768
r_sphericity_free	8.671
r_scangle_it	4.751
r_dihedral_angle_1_deg	4.677
r_scbond_it	3.516
r_sphericity_bonded	2.638
r_rigid_bond_restr	2.259
r_mcangle_it	2.215
r_mcbond_it	1.973
r_angle_refined_deg	1.558
r_angle_other_deg	0.89
r_mcbond_other	0.605
r_symmetry_hbond_refined	0.315
r_symmetry_vdw_refined	0.253
r_symmetry_vdw_other	0.236
r_nbd_refined	0.229
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.182
r_nbd_other	0.179
r_chiral_restr	0.108
r_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2771
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	86

Software

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