Experiment: 3DH9

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1 M MES, 20% PEG 4000, pH 5.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.971	α = 90
b = 150.971	β = 90
c = 267.706	γ = 120

Symmetry
Space Group	H 3 2

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	MAR CCD 165 mm	mirrors	2008-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.979	NSLS	X4C

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	2.25	32	100	0.089	8	12.3		55708

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	2.25	2.33	100		0.438	5.38	11.3	5517

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.25	31.17	55705	5611	99.98	0.184	0.177	0.19	0.248	0.25	RANDOM	14.901

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]
0.48	0.24		0.48		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.563
r_dihedral_angle_4_deg	19.26
r_dihedral_angle_3_deg	18.558
r_dihedral_angle_1_deg	6.961
r_scangle_it	3.908
r_scbond_it	2.601
r_angle_refined_deg	2.045
r_mcangle_it	1.492
r_mcbond_it	0.953
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.563
r_dihedral_angle_4_deg	19.26
r_dihedral_angle_3_deg	18.558
r_dihedral_angle_1_deg	6.961
r_scangle_it	3.908
r_scbond_it	2.601
r_angle_refined_deg	2.045
r_mcangle_it	1.492
r_mcbond_it	0.953
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.242
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.22
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.165
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7384
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	106

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Custom pXSCAN motion control software coupled with the Mar345 data collection software	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.