4IEG | pdb_00004ieg

Structure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12 (P1 crystal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GZK	PDB ENTRY 4GZK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.2 M Mg formate 20% PEG 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.874	α = 75.16
b = 94.47	β = 63.11
c = 96.481	γ = 83.79

Symmetry
Space Group	P 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	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	2.1	50	92.6	0.048	17.8	1.9	156487	144893		-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	2.1	2.14	87.1		0.202	2.9	1.7	7802

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 4GZK	2.1	50	156991	137611	7276	92.29	0.22	0.22025	0.2172	0.22	0.27836	0.29	RANDOM	27.467

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]
-0.1	0.62	-0.17	0.57	-0.53	-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.418
r_dihedral_angle_4_deg	17.032
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	5.646
r_scangle_it	1.818
r_scbond_it	1.112
r_angle_refined_deg	1.1
r_angle_other_deg	0.817
r_mcangle_it	0.685
r_mcbond_it	0.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.418
r_dihedral_angle_4_deg	17.032
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	5.646
r_scangle_it	1.818
r_scbond_it	1.112
r_angle_refined_deg	1.1
r_angle_other_deg	0.817
r_mcangle_it	0.685
r_mcbond_it	0.366
r_mcbond_other	0.074
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20846
Nucleic Acid Atoms
Solvent Atoms	1655
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	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 R01GM157729.