Experiment: 2HVY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	303	30% MPD, 35mM CH3COOMg, 10mM ATP, 50mM cacodylate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.031	α = 90
b = 90.95	β = 90
c = 114.064	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2006-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	2.3	20	99.7	0.055	38	6.8	39340	39234		-3

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	2.3	2.34	100		0.331	6.7	7.3	1950

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2EY4	2.3	20	37072	36983	1914	99.76	0.23984	0.23984	0.23786	0.23	0.27807	0.27	RANDOM	43.191

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]
-0.27			2.4		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.482
r_dihedral_angle_4_deg	15.315
r_dihedral_angle_3_deg	14.902
r_dihedral_angle_1_deg	4.815
r_angle_refined_deg	1.045
r_scangle_it	0.641
r_scbond_it	0.379
r_mcangle_it	0.341
r_nbtor_refined	0.288
r_mcbond_it	0.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.482
r_dihedral_angle_4_deg	15.315
r_dihedral_angle_3_deg	14.902
r_dihedral_angle_1_deg	4.815
r_angle_refined_deg	1.045
r_scangle_it	0.641
r_scbond_it	0.379
r_mcangle_it	0.341
r_nbtor_refined	0.288
r_mcbond_it	0.193
r_nbd_refined	0.155
r_symmetry_vdw_refined	0.134
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.081
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4512
Nucleic Acid Atoms	1235
Solvent Atoms	118
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
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.