Experiment: 3IB4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z9T	PDB ENTRY 2z9t

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1M NaAcetate, 0.2M CH3COONH4, 20% Glycerol, 22% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 28.58	β = 132.87
c = 60.73	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 210	Sagitally focusing Ge(220) and a multilayer	2009-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

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	1.25	19.04	99.6	0.1	15.5	10		26776			8.213

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)
	1.25	1.32	97.2		0.692	3.2	8.7	3812

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2z9t	1.25	15	25414	1355	99.56	0.15904	0.15784	0.16	0.18118	0.19	RANDOM	10.92

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]
-0.05		-0.04	0.04		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.3
r_dihedral_angle_4_deg	18.703
r_dihedral_angle_3_deg	12.255
r_dihedral_angle_1_deg	7.14
r_sphericity_free	3.24
r_sphericity_bonded	2.377
r_scangle_it	2.372
r_mcangle_it	2.194
r_scbond_it	1.694
r_mcbond_it	1.466

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.3
r_dihedral_angle_4_deg	18.703
r_dihedral_angle_3_deg	12.255
r_dihedral_angle_1_deg	7.14
r_sphericity_free	3.24
r_sphericity_bonded	2.377
r_scangle_it	2.372
r_mcangle_it	2.194
r_scbond_it	1.694
r_mcbond_it	1.466
r_angle_refined_deg	1.399
r_rigid_bond_restr	1.073
r_chiral_restr	0.103
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	826
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.