Experiment: 3LW8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S1C	PDB ENTRY 1S1C, partially refined structure of free IpgB2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	20% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.59	α = 90
b = 101.6	β = 96.43
c = 97.03	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	CCD	MARMOSAIC 225 mm CCD		2009-07-27	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)	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	1.85	48.21	98.4	0.052	15.11	3.5		133487		-3	26.4

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	1.85	1.9	97.8		0.492	2.5	2.6	9777

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	PDB ENTRY 1S1C, partially refined structure of free IpgB2	1.85	48.2	133481	6674	98.42	0.18	0.177	0.233	RANDOM	21.609

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]
-0.45		-0.29	1.47		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.973
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_3_deg	15.15
r_dihedral_angle_1_deg	5.217
r_scangle_it	3.45
r_scbond_it	2.153
r_angle_refined_deg	1.423
r_mcangle_it	1.361
r_mcbond_it	0.777
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.973
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_3_deg	15.15
r_dihedral_angle_1_deg	5.217
r_scangle_it	3.45
r_scbond_it	2.153
r_angle_refined_deg	1.423
r_mcangle_it	1.361
r_mcbond_it	0.777
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11613
Nucleic Acid Atoms
Solvent Atoms	1766
Heterogen Atoms	116

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.