2RCC | pdb_00002rcc

Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from Bacillus halodurans at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 10.0% Glycerol, 5.0% PEG 3000, 30.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.26	α = 90
b = 72.78	β = 124.9
c = 111.77	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-07-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926	SSRL	BL11-1

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	1.9	28.502	98.2	0.055	7.13			90521		-3	27.44

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	1.9	1.97	97		0.389	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	1.9	28.502	90520	4538	99.52	0.184	0.183	0.19	0.215	0.21	RANDOM	19.585

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]
-1.23		-0.95	-0.46		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.801
r_dihedral_angle_4_deg	17.402
r_dihedral_angle_3_deg	12.015
r_scangle_it	7.089
r_scbond_it	5.537
r_dihedral_angle_1_deg	3.635
r_mcangle_it	2.932
r_mcbond_it	2.158
r_angle_refined_deg	1.613
r_angle_other_deg	1.292
r_mcbond_other	0.578
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.194
r_symmetry_vdw_other	0.187
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.144
r_nbd_other	0.141
r_chiral_restr	0.092
r_nbtor_other	0.088
r_metal_ion_refined	0.071
r_xyhbond_nbd_other	0.063
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7328
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing