Experiment: 2H4H

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YC5	PDB Entry: 1yc5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.6	293	CHES, PEG 3350, pH9.6, NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.26	α = 90
b = 58.676	β = 90
c = 106.846	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 4		2005-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D		APS	14-BM-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.4	0.099		6.7		20058	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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: 1yc5	1.99	50	2	18900	17895	1015	99.75	0.1977	0.19559	0.23683	RANDOM	24.435

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]
2.18			-0.73		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.361
r_dihedral_angle_4_deg	24.716
r_dihedral_angle_3_deg	14.269
r_dihedral_angle_1_deg	6.096
r_scangle_it	4.365
r_scbond_it	2.84
r_angle_refined_deg	1.947
r_mcangle_it	1.855
r_mcbond_it	1.12
r_nbtor_refined	0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.361
r_dihedral_angle_4_deg	24.716
r_dihedral_angle_3_deg	14.269
r_dihedral_angle_1_deg	6.096
r_scangle_it	4.365
r_scbond_it	2.84
r_angle_refined_deg	1.947
r_mcangle_it	1.855
r_mcbond_it	1.12
r_nbtor_refined	0.332
r_symmetry_hbond_refined	0.295
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.265
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1908
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	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 R01GM133198.