2B4A | pdb_00002b4a

Crystal structure of a response regulator receiver domain protein (bh3024) from bacillus halodurans c-125 at 2.42 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KGS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.2	277	0.2M NaCl, 10.0% PEG-8000, 0.1M Na, K-Phosphate, pH 6.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.003	α = 90
b = 39.003	β = 90
c = 172.741	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	ADSC QUANTUM 315	flat mirror	2005-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.36	28.94	98	0.086	0.086	6	10.9		5994

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.42		84.8	0.71	0.71	1.1	3.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	1kgs	2.42	28.94	5309	257	98.78	0.185	0.182	0.19	0.243	0.25	RANDOM	30.123

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]
0.68			0.68		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.418
r_dihedral_angle_4_deg	27.805
r_dihedral_angle_3_deg	15.545
r_scangle_it	8.326
r_dihedral_angle_1_deg	8.017
r_scbond_it	6.309
r_mcangle_it	3.815
r_mcbond_it	2.372
r_angle_refined_deg	1.732
r_angle_other_deg	0.995
r_mcbond_other	0.443
r_symmetry_vdw_other	0.247
r_nbd_refined	0.211
r_nbd_other	0.195
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.145
r_symmetry_vdw_refined	0.116
r_chiral_restr	0.104
r_nbtor_other	0.094
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	889
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing