Experiment: 2HDF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	7-8 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.001M EDTA, 0.3M NACL, 1% N-OCTYL-2-HYDROXYETHYL SULFOXIDE MIXED AT 1:1 RATIO WITH 0.1M TRIS PH7.5, 0.02-0.05M SRCL2, 5% ISOPROPANOL, 32-40 % PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.593	α = 90
b = 84.336	β = 109.16
c = 99.458	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	MARMOSAIC 225 mm CCD		2003-07-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97940, 0.97924, 0.97240	APS	22-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	2.65	30	99.1	0.095	16.4	3.7	40440	40440

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	2.65	2.74	91.8		0.645	1.85	2	3745

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.65	15	19508	19508	1056	99.99	0.24137	0.24137	0.23867	0.2911	RANDOM	57.581

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]
2.67		1.2	0.36		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.544
r_dihedral_angle_3_deg	18.502
r_dihedral_angle_4_deg	16.523
r_dihedral_angle_1_deg	6.505
r_scangle_it	6.136
r_scbond_it	4.056
r_mcangle_it	3.311
r_mcbond_it	1.936
r_angle_refined_deg	1.303
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.544
r_dihedral_angle_3_deg	18.502
r_dihedral_angle_4_deg	16.523
r_dihedral_angle_1_deg	6.505
r_scangle_it	6.136
r_scbond_it	4.056
r_mcangle_it	3.311
r_mcbond_it	1.936
r_angle_refined_deg	1.303
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4493
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
SHARP	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.