Experiment: 3PUP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	277	100 mM Tris pH 7.4 20 % PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.32	α = 90
b = 84.3	β = 90
c = 178.12	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 225 mm CCD		2010-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.99	49.33	97.3	0.186	0.186	6.3	5	25974	25273			59.6

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	2.99	3.15	97.7		0.772	0.772	1	4.9	3651

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2JLD	2.99	49.33	26104	25227	1274	96.64	0.2064	0.2064	0.2042	0.21	0.2489	0.25	RANDOM	51.9741

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]
0.61			4.89		-5.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.387
r_dihedral_angle_4_deg	16.555
r_sphericity_bonded	16.18
r_dihedral_angle_3_deg	15.307
r_scangle_it	9.525
r_scbond_it	6.813
r_dihedral_angle_1_deg	6.132
r_mcangle_it	4.18
r_mcbond_it	2.452
r_angle_refined_deg	1.516

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.387
r_dihedral_angle_4_deg	16.555
r_sphericity_bonded	16.18
r_dihedral_angle_3_deg	15.307
r_scangle_it	9.525
r_scbond_it	6.813
r_dihedral_angle_1_deg	6.132
r_mcangle_it	4.18
r_mcbond_it	2.452
r_angle_refined_deg	1.516
r_mcbond_other	1.192
r_angle_other_deg	0.971
r_chiral_restr	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5324
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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.