4GZK

Structure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	4 M Na formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.805	α = 90
b = 72.32	β = 90
c = 96.828	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	MAR CCD 165 mm		2012-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.979	NSLS	X4C

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	1.69	50	99.9	0.069	39.5	14.3	105727	105656		-3

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	1.7	1.73	100		0.411	6.1	11.7	5246

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.69	32.85	106066	105419	5224	99.39	0.13	0.13139	0.12953	0.16718	RANDOM	16.512

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]
-0.14			0.36		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.147
r_dihedral_angle_4_deg	19.364
r_dihedral_angle_3_deg	11.661
r_scangle_it	5.982
r_dihedral_angle_1_deg	5.865
r_scbond_it	3.969
r_mcangle_it	2.496
r_rigid_bond_restr	1.599
r_angle_refined_deg	1.533
r_mcbond_it	1.529

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.147
r_dihedral_angle_4_deg	19.364
r_dihedral_angle_3_deg	11.661
r_scangle_it	5.982
r_dihedral_angle_1_deg	5.865
r_scbond_it	3.969
r_mcangle_it	2.496
r_rigid_bond_restr	1.599
r_angle_refined_deg	1.533
r_mcbond_it	1.529
r_angle_other_deg	0.955
r_mcbond_other	0.467
r_chiral_restr	0.099
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5257
Nucleic Acid Atoms
Solvent Atoms	1166
Heterogen Atoms	8

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.