Experiment: 3DZO

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.8	293	22% PEG 4000, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.261	α = 90
b = 44.288	β = 98.9
c = 105.304	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 300 mm CCD		2008-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.96749	APS	23-ID-D

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	1.8	40	97.6	0.049	0.06	173	3.6	34415	34415			33.586

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	1.8	1.86	81.4		0.2	0.151	4.23	2.6	2820

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BYV	1.8	35	34337	34337	1717	97.63	0.246	0.246	0.244	0.24	0.27	RANDOM	31.279

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]
-2.94		-0.28	1.88		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.732
r_dihedral_angle_4_deg	18.405
r_dihedral_angle_3_deg	14.645
r_dihedral_angle_1_deg	5.049
r_scangle_it	1.52
r_angle_refined_deg	1.069
r_scbond_it	1.005
r_mcangle_it	0.621
r_mcbond_it	0.363
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.732
r_dihedral_angle_4_deg	18.405
r_dihedral_angle_3_deg	14.645
r_dihedral_angle_1_deg	5.049
r_scangle_it	1.52
r_angle_refined_deg	1.069
r_scbond_it	1.005
r_mcangle_it	0.621
r_mcbond_it	0.363
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.199
r_nbd_refined	0.185
r_metal_ion_refined	0.157
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2678
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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.