4DJA | pdb_00004dja

Crystal structure of a prokaryotic (6-4) photolyase PhrB from Agrobacterium Tumefaciens with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore at 1.45A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		UNPUBLISHED STRUCTURAL DATA OF FE-EDGE SAD-PHASING (WAVELENGTH:1.741) - 2ND CRYSTAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	100 mM MES, 4% PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.388	α = 90
b = 106.786	β = 90
c = 55.913	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 225 mm CCD	mirrors	2011-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	1.45	72.36	95.6	0.037	22	4.4	104964	104964			15.9

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	1.45	1.53	78		0.377	2.7	3.1	11597

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 (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X-RAY DIFFRACTION	SAD/MOLECULAR REPLACEMENT	THROUGHOUT	UNPUBLISHED STRUCTURAL DATA OF FE-EDGE SAD-PHASING (WAVELENGTH:1.741) - 2ND CRYSTAL	1.45	19.95	99709	92395	4874	92.67	0.13995	0.13995	0.13779	0.14	0.18049	0.18	RANDOM	19.13

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]
0.01			-0.04		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.183
r_dihedral_angle_4_deg	17.228
r_dihedral_angle_3_deg	12.293
r_dihedral_angle_1_deg	5.198
r_angle_refined_deg	1.517
r_chiral_restr	0.126
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4089
Nucleic Acid Atoms
Solvent Atoms	836
Heterogen Atoms	97

Software

Software
Software Name	Purpose
MAR345	data collection
SHELXCD	phasing
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.