Experiment: 2HDZ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 277K
2	VAPOR DIFFUSION, HANGING DROP	7.5	277	Se-Met derivate, pH 7.5, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.812	α = 90
b = 60.812	β = 90
c = 63.158	γ = 120

Symmetry
Space Group	P 65

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 210		2004-08-24	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm		2005-05-03	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9363	CHESS	A1
2	SYNCHROTRON	BSRF BEAMLINE 3W1A	0.97985	BSRF	3W1A

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
1,2	2	30	99.3	0.046	0.049	35.6	11.1	9000	8917	2	2

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	2	2.03	93.3		0.185		10	431

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	SAD	THROUGHOUT	2	10	8492	8492	425	99.49	0.22	0.21953	0.217	0.267	RANDOM	28.535

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]
2.21	1.11		2.21		-3.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.991
r_dihedral_angle_4_deg	16.373
r_dihedral_angle_3_deg	11.677
r_dihedral_angle_1_deg	4.993
r_scangle_it	4.539
r_scbond_it	3.009
r_mcangle_it	1.504
r_angle_refined_deg	1.446
r_mcbond_it	1.114
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.991
r_dihedral_angle_4_deg	16.373
r_dihedral_angle_3_deg	11.677
r_dihedral_angle_1_deg	4.993
r_scangle_it	4.539
r_scbond_it	3.009
r_mcangle_it	1.504
r_angle_refined_deg	1.446
r_mcbond_it	1.114
r_nbtor_refined	0.294
r_symmetry_hbond_refined	0.27
r_xyhbond_nbd_refined	0.219
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	561
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.