3K8T | pdb_00003k8t

Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CVX	PDB ENTRY 2CVX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	100MM HEPES, PH7.5, 20-25% PEG 3350, 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.528	α = 90
b = 116.915	β = 90
c = 64.065	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	ADSC QUANTUM 315		2006-12-12	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARMOSAIC 300 mm CCD		2007-03-10	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C
2	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

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	0.164	8.47	6.9		47632

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)
1,2	2.1	2.18	96.8		0.423	2.41	3.8

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 2CVX	2.1	38.84	45193	2409	99.3	0.254	0.252	0.25	0.29	0.29	RANDOM	50.59

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]
-2.17			-1.51		3.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.829
r_dihedral_angle_3_deg	18.786
r_dihedral_angle_4_deg	18.205
r_dihedral_angle_1_deg	7
r_scangle_it	2.799
r_scbond_it	2.034
r_angle_refined_deg	1.719
r_mcangle_it	1.288
r_mcbond_it	1.074
r_angle_other_deg	0.939
r_xyhbond_nbd_other	0.272
r_symmetry_vdw_other	0.24
r_mcbond_other	0.217
r_nbd_refined	0.214
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.113
r_nbtor_other	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5120
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	67

Software

Software
Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing