Experiment: 7PPG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GVJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	1 microliter of protein mixed with 1 microliter of reservoir buffer (27-31% PEG 3350 (w/v), 200 mM NaCl, 100 mM sodium dihydrogen phosphate pH 7.6) incubated for 5 min, then streak seeded (with crystals obtained previously under identical conditions). Ligand added prior to crystallization (2 MILLIMOLAR FROM 100 MILLIMOLAR STOCK IN DMSO) and incubated for 1.5 h at 277 K. CRYO BUFFER consisted of RESERVOIR supplemented WITH 2 MILLIMOLAR INHIBITOR AND 15% ETHYLENGLYCOL

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.956	α = 90
b = 106.18	β = 96.53
c = 121.34	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2014-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	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	2.13	48.59	98	0.121	0.151	0.994	6.89	2.67		114934			24.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.26	96.1		0.459	0.57	0.854	2.2	2.7

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	2GVJ	2.13	48.59	109187	5747	97.97	0.2553	0.2528	0.26	0.3025	0.31	RANDOM	20.514

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]
-0.76		-0.65	-0.2		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.735
r_dihedral_angle_4_deg	16.37
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	6.907
r_angle_refined_deg	1.422
r_angle_other_deg	1.286
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.735
r_dihedral_angle_4_deg	16.37
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	6.907
r_angle_refined_deg	1.422
r_angle_other_deg	1.286
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14937
Nucleic Acid Atoms
Solvent Atoms	1329
Heterogen Atoms	175

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
pointless	data scaling
PHASER	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.