3GQA | pdb_00003gqa

Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with cobalt ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10.5	298	100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the apo-crystals in a mother liquid containing 10mM cobalt ions, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.741	α = 90
b = 89.741	β = 90
c = 584.795	γ = 120

Symmetry
Space Group	H 3 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	MARMOSAIC 300 mm CCD		2008-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.98	APS	23-ID-D

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	43.88	99.5	0.099	31.667	8.5		53528

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	2.18	100		0.555		8.7	5279

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	3GQ7	2.1	43.88	53508	2708	99.49	0.182	0.18	0.18	0.222	0.22	RANDOM	29.128

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]
1.83	0.92		1.83		-2.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.907
r_dihedral_angle_4_deg	16.783
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	6.996
r_scangle_it	3.174
r_scbond_it	2.058
r_angle_refined_deg	1.377
r_mcangle_it	1.121
r_mcbond_it	0.691
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.907
r_dihedral_angle_4_deg	16.783
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	6.996
r_scangle_it	3.174
r_scbond_it	2.058
r_angle_refined_deg	1.377
r_mcangle_it	1.121
r_mcbond_it	0.691
r_nbtor_refined	0.308
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.187
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4473
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.