Experiment: 3GPN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PLQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	291	1.6 M ammonium sulfate and 0.1 M sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.97	68.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.59	α = 90
b = 147.509	β = 90
c = 81.442	γ = 90

Symmetry
Space Group	C 2 2 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	NOIR-1	saggital focusing mirrors	2008-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.072	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	81.38	98.18	0.09	11.4	4.75	15940	14864			42.619

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)
	2.5	2.565	96.79		0.365	0.365	3.2	4.75	1041

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1PLQ	2.5	81.38	0.02	14864	14864	784	98.18	0.23636	0.23443	0.2734	RANDOM	42.619

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]
-0.04			-1.2		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.295
r_dihedral_angle_3_deg	19.03
r_dihedral_angle_4_deg	12.811
r_dihedral_angle_1_deg	7.264
r_scangle_it	3.513
r_scbond_it	2.182
r_mcangle_it	1.716
r_angle_refined_deg	1.676
r_mcbond_it	0.975
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.295
r_dihedral_angle_3_deg	19.03
r_dihedral_angle_4_deg	12.811
r_dihedral_angle_1_deg	7.264
r_scangle_it	3.513
r_scbond_it	2.182
r_mcangle_it	1.716
r_angle_refined_deg	1.676
r_mcbond_it	0.975
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.101
r_symmetry_hbond_refined	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1979
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	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.