2ZLG | pdb_00002zlg

The Structual Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase

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, 20-25% PEG3350, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.789	α = 90
b = 116.565	β = 90
c = 63.641	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		2006-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	2.52	79.06	98.3	0.074	18.8	4.7		27055

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	2.522	2.587	92.4		0.461	2.4	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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2CVX	2.52	49.6	25564	1359	97.03	0.21916	0.21553	0.2919	0.2802	RANDOM	41.129

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]
-5.59			-2.7		8.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.4
r_dihedral_angle_3_deg	18.319
r_dihedral_angle_4_deg	15.686
r_scangle_it	7.1
r_dihedral_angle_1_deg	6.147
r_scbond_it	5.412
r_mcangle_it	5.176
r_mcbond_it	3.845
r_angle_refined_deg	1.421
r_nbtor_refined	0.333
r_nbd_refined	0.256
r_symmetry_vdw_refined	0.24
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.088
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5228
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	87

Software

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