2ZLF | pdb_00002zlf

The Structural 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% PEG 3350, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.948	α = 90
b = 116.999	β = 90
c = 63.873	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	mirrors	2007-03-01	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	2.59	50	96.5	0.081	21.5	6.6		24929		2

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)
	2.589	2.656	82.4		0.459	2.1	5.8

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	2.59	49.75	23611	1262	96.05	0.19554	0.19249	0.1901	0.25143	0.2497	RANDOM	36.936

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]
-3.11			-2.67		5.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_4_deg	19.282
r_dihedral_angle_3_deg	19.236
r_scangle_it	6.577
r_dihedral_angle_1_deg	6.494
r_scbond_it	4.916
r_mcangle_it	4.623
r_mcbond_it	3.266
r_angle_refined_deg	1.459
r_nbtor_refined	0.334
r_nbd_refined	0.251
r_symmetry_vdw_refined	0.243
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.1
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5354
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms

Software

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