2D0S | pdb_00002d0s

Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	30% (w/v) polyethylene glycol 4000, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.25	α = 90
b = 58.413	β = 90
c = 56.315	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	RIGAKU RAXIS IV++	confocal mirror optics	2004-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	2.2	50	94.4	0.08	17.65	4.4	4086	4086	2	2

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)
	2.2	2.28	75.3		0.184	4.67	3.9	314

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.2	9.74	2	3898	4025	378	94.16	0.181	0.184	0.181	0.1559	0.218	0.1539	RANDOM	20.466

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]
0.03			-0.1		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.356
r_dihedral_angle_3_deg	20.803
r_dihedral_angle_1_deg	7.789
r_scangle_it	4.486
r_dihedral_angle_4_deg	4.477
r_mcangle_it	4.014
r_scbond_it	3.07
r_mcbond_it	2.574
r_angle_refined_deg	1.434
r_nbtor_refined	0.326
r_nbd_refined	0.297
r_symmetry_vdw_refined	0.275
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.119
r_bond_refined_d	0.023
r_gen_planes_refined	0.017
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	600
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing