Experiment: 3GPH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E61	PDB entry 3E61

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.709	α = 90
b = 70.709	β = 90
c = 222.823	γ = 90

Symmetry
Space Group	P 43

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	Sagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror	2008-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.000	APS	17-BM

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	2.7	50	95.4	0.104	17.071	6.7	28495	28493			51.075

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)
	2.7	2.8	93.4		0.457		6.3	2034

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3E61	2.7	31.31	27040	1442	95.49	0.21609	0.21245	0.28261	RANDOM	28.748

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.537
r_dihedral_angle_4_deg	24.048
r_dihedral_angle_3_deg	21.783
r_dihedral_angle_1_deg	7.517
r_scangle_it	2.797
r_angle_refined_deg	1.909
r_scbond_it	1.828
r_mcangle_it	1.172
r_mcbond_it	0.677
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.537
r_dihedral_angle_4_deg	24.048
r_dihedral_angle_3_deg	21.783
r_dihedral_angle_1_deg	7.517
r_scangle_it	2.797
r_angle_refined_deg	1.909
r_scbond_it	1.828
r_mcangle_it	1.172
r_mcbond_it	0.677
r_nbtor_refined	0.315
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.206
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.136
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7530
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	120

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.