3RRI | pdb_00003rri

Crystal structure of glyoxalase/bleomycin resistance protein/dioxygenase from Alicyclobacillus acidocaldarius

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		different crystal form of the same protein that was solved by SAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.1 M Bis/Tris propane:NaOH, 2.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.728	α = 90
b = 104.728	β = 90
c = 49.77	γ = 90

Symmetry
Space Group	I 4

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 315r	mirrors	2011-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932	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	1.5	50	99.6	0.093	32	10	43462	43267		-3	20.1

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	1.5	1.53	99.6		0.827	2.5	7.4	2167

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	MOLECULAR REPLACEMENT	THROUGHOUT	different crystal form of the same protein that was solved by SAD	1.5	50	43211	42129	1082	99.36	0.13563	0.13563	0.13504	0.14	0.15911	0.16	according to the highest possible lattice symmetry	19.261

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]
-10.82			-10.82		21.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.072
r_dihedral_angle_4_deg	24.101
r_dihedral_angle_3_deg	13.606
r_dihedral_angle_1_deg	6.603
r_scangle_it	3.515
r_scbond_it	2.227
r_mcangle_it	1.5
r_angle_refined_deg	1.47
r_mcbond_it	0.849
r_angle_other_deg	0.848

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.072
r_dihedral_angle_4_deg	24.101
r_dihedral_angle_3_deg	13.606
r_dihedral_angle_1_deg	6.603
r_scangle_it	3.515
r_scbond_it	2.227
r_mcangle_it	1.5
r_angle_refined_deg	1.47
r_mcbond_it	0.849
r_angle_other_deg	0.848
r_mcbond_other	0.243
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2288
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	8

Software

Software
Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.