Experiment: 3LCE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E4D	PDB entry 1e4d

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	1.4 M sodium potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.7	α = 90
b = 82.544	β = 94.63
c = 102.36	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	IMAGE PLATE	MAR scanner 345 mm plate		2008-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.917	102.062	97.3	0.082	0.082	13.9	3.4	84571	84571

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	2.12	99.3		0.35	0.35	2.2	3.4	11881

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	REFMAC rigid body refinement	THROUGHOUT	PDB entry 1e4d	2	102.06	73266	3651	99.36	0.181	0.178	0.233	RANDOM	20.045

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]
0.24		-0.48	-0.12		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.482
r_dihedral_angle_4_deg	19.711
r_dihedral_angle_3_deg	15.033
r_dihedral_angle_1_deg	5.663
r_scangle_it	4.903
r_scbond_it	3.025
r_angle_refined_deg	1.78
r_mcangle_it	1.738
r_mcbond_it	0.99
r_chiral_restr	0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.482
r_dihedral_angle_4_deg	19.711
r_dihedral_angle_3_deg	15.033
r_dihedral_angle_1_deg	5.663
r_scangle_it	4.903
r_scbond_it	3.025
r_angle_refined_deg	1.78
r_mcangle_it	1.738
r_mcbond_it	0.99
r_chiral_restr	0.126
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7862
Nucleic Acid Atoms
Solvent Atoms	917
Heterogen Atoms	106

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
REFMAC	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.