1YFD | pdb_00001yfd

Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	PEG 4000, 0.1M MES, 0.4M NACL, 1mM EMTS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.04	α = 90
b = 84.74	β = 90
c = 115.03	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		1997-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A	0.873	ESRF	BM1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	19.6	99.1	0.084	10.8	3.3		57178			17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2	98.4		0.233	6.8

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 (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	pdb entry 1PFR	1.9	19.46	54865	2312	99.18	0.17449	0.17314	0.18	0.20601	0.21	RANDOM	16.662

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]
-0.82			0.31		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.339
r_dihedral_angle_4_deg	15.278
r_dihedral_angle_3_deg	14.547
r_dihedral_angle_1_deg	5.143
r_scangle_it	2.823
r_scbond_it	1.99
r_angle_refined_deg	1.353
r_mcangle_it	1.153
r_mcbond_it	0.997
r_angle_other_deg	0.897
r_metal_ion_refined	0.257
r_nbd_refined	0.227
r_symmetry_vdw_other	0.22
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.178
r_mcbond_other	0.175
r_symmetry_hbond_refined	0.165
r_symmetry_vdw_refined	0.126
r_nbtor_other	0.086
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
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	5578
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
XFIT	data reduction