Experiment: 3PDB

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	20% PEG 4000, 100 mM ammonium sulphate, 6% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 282.418	α = 90
b = 77.894	β = 90
c = 87.389	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315		2007-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	2.4	30		0.12		10.3		76929

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)
1	2.4	2.49			0.32		3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3hlm	2.4	30	67047	3554	92.77	0.1776	0.17692	0.19047	RANDOM	28.273

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.319
r_dihedral_angle_4_deg	19.034
r_dihedral_angle_3_deg	16.716
r_dihedral_angle_1_deg	6.031
r_scangle_it	3.951
r_scbond_it	2.403
r_angle_refined_deg	1.597
r_mcangle_it	1.365
r_mcbond_it	0.69
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.319
r_dihedral_angle_4_deg	19.034
r_dihedral_angle_3_deg	16.716
r_dihedral_angle_1_deg	6.031
r_scangle_it	3.951
r_scbond_it	2.403
r_angle_refined_deg	1.597
r_mcangle_it	1.365
r_mcbond_it	0.69
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12590
Nucleic Acid Atoms
Solvent Atoms	706
Heterogen Atoms	99

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.