3GQH | pdb_00003gqh

Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	100mM Bis-Tris at pH 7.0, 20% PEG4K and 10% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.144	α = 90
b = 84.158	β = 90
c = 86.228	γ = 90

Symmetry
Space Group	P 21 21 21

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	1.03	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	42.08	99.5	0.087	0.087	29.1			55084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	100		0.438	0.438	7		5419

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.8	42.08	54993	2795	99.44	0.229	0.228	0.23	0.256	0.26	RANDOM	26.743

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]
0.34			-0.48		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.661
r_dihedral_angle_4_deg	17.754
r_dihedral_angle_3_deg	14.586
r_dihedral_angle_1_deg	5.832
r_scangle_it	3.228
r_scbond_it	2.055
r_mcangle_it	1.554
r_angle_refined_deg	1.197
r_mcbond_it	0.928
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.661
r_dihedral_angle_4_deg	17.754
r_dihedral_angle_3_deg	14.586
r_dihedral_angle_1_deg	5.832
r_scangle_it	3.228
r_scbond_it	2.055
r_mcangle_it	1.554
r_angle_refined_deg	1.197
r_mcbond_it	0.928
r_nbtor_refined	0.308
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.186
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3815
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.