2OOL | pdb_00002ool

Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome RpBphP3 from R. palustris

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZTU	modified PDB entry 1ZTU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	protein concentration of 12mg/ml in 100 mM tri-sodium citrate pH 5.6, 6% isopropanol (v/v), and 7% PEG 4000 (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.866	α = 90
b = 151.866	β = 90
c = 75.996	γ = 120

Symmetry
Space Group	P 3 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	100	CCD	ADSC QUANTUM 315		2006-02-22	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-02-09	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.97	APS	19-ID

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	2.1	50	99.3	0.077	10.7	13.9	59009	58049

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.1	2.18	100			11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	modified PDB entry 1ZTU	2.2	49.75	51388	43956	3595	93.29	0.19157	0.18828	0.19	0.23102	0.23	RANDOM	47.92

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]
2.38	1.19		2.38		-3.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.836
r_dihedral_angle_4_deg	18.399
r_dihedral_angle_3_deg	16.567
r_dihedral_angle_1_deg	6.508
r_scangle_it	2.671
r_scbond_it	1.965
r_angle_refined_deg	1.579
r_mcangle_it	1.235
r_mcbond_it	1.075
r_angle_other_deg	0.982
r_symmetry_vdw_refined	0.461
r_symmetry_vdw_other	0.425
r_nbd_refined	0.21
r_nbd_other	0.202
r_mcbond_other	0.186
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.154
r_chiral_restr	0.096
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4731
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	86

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
14BMC	data collection
HKL-2000	data reduction