3HO7 | pdb_00003ho7

Crystal structure of OxyR from Porphyromonas gingivalis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291.15	12% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
2	VAPOR DIFFUSION, SITTING DROP	7.5	291.15	12% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.819	α = 110.63
b = 55.795	β = 102.82
c = 56.711	γ = 114.63

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++	MSC Varimax confocal optics	2009-02-04	M	SINGLE WAVELENGTH
2	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++	MSC Varimax confocal optics	2009-03-19	M	SINGLE WAVELENGTH
3	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++	MSC Varimax confocal optics	2009-03-27	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418
2	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418
3	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
1,2,3	1.58	26.94	86.2	0.032		3.92	127008	59646	3	3.7

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)
1,2,3	1.58		86.2		0.032		3.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1.58	26.94	59646	57380	2033	83.56	0.22028	0.2194	0.2694	0.24456	RANDOM	33.429

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]
1.25	0.59	-6.77	1.22	5.57	-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.562
r_dihedral_angle_3_deg	11.367
r_dihedral_angle_4_deg	10.566
r_dihedral_angle_1_deg	4.283
r_scangle_it	0.856
r_angle_refined_deg	0.648
r_scbond_it	0.538
r_mcangle_it	0.385
r_mcbond_it	0.21
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	3534
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
REFMAC	refinement
d*TREK	data reduction
CrystalClear	data scaling
PHENIX	phasing