Experiment: 3BD0

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	Crystal was grown in 22.5% PEG 3350, 0.1 M MES pH 5.5. Soaked in 5 mM ZnCl2, 22.5% PEG 3350 pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.877	α = 90
b = 88.307	β = 90
c = 97.051	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		CCD	MAR CCD 165 mm		2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97989	APS	31-ID

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	3	30	99.9	0.227	3.5	7.2		24559

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)
	3	3.11	99.8		0.626		6.5	2404

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 3BCZ	3.01	29.68	24472	1249	99.42	0.217	0.213	0.28	RANDOM	19.753

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]
-1.45			3.57		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.671
r_dihedral_angle_3_deg	19.221
r_dihedral_angle_4_deg	17.874
r_dihedral_angle_1_deg	5.625
r_scangle_it	2.148
r_angle_refined_deg	1.33
r_scbond_it	1.258
r_mcangle_it	0.944
r_mcbond_it	0.614
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.671
r_dihedral_angle_3_deg	19.221
r_dihedral_angle_4_deg	17.874
r_dihedral_angle_1_deg	5.625
r_scangle_it	2.148
r_angle_refined_deg	1.33
r_scbond_it	1.258
r_mcangle_it	0.944
r_mcbond_it	0.614
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.278
r_symmetry_hbond_refined	0.253
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9356
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.