3N6M | pdb_00003n6m

Crystal structure of EV71 RdRp in complex with GTP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.494	α = 90
b = 103.494	β = 90
c = 133.049	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM 270		2009-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

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	2.5	89.8	97	0.095				32854

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	2.5	2.6	97		0.53

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.5	50	32855	27582	1486	99.96	0.20112	0.19671	0.19393	0.1928	0.24897	0.2449	RANDOM	43.933

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]
0.39	0.2		0.39		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.856
r_dihedral_angle_3_deg	19.492
r_dihedral_angle_4_deg	19.126
r_dihedral_angle_1_deg	6.532
r_scangle_it	3.125
r_scbond_it	1.96
r_mcangle_it	1.559
r_angle_refined_deg	1.514
r_mcbond_it	0.859
r_nbtor_refined	0.313
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3700
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	33

Software

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