Experiment: 1YH2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JBB	pdb entry 1JBB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	4M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.45	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.831	α = 90
b = 54.831	β = 90
c = 183.279	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IV		2004-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	40	99.5	0.036	44.8	5.1	19774	19774		-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	2.07	98		0.266		3.9	1885

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	pdb entry 1JBB	2	20	18669	1007	99.54	0.20372	0.2019	0.21	0.23793	0.24	RANDOM	37.992

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]
1.63			1.63		-3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.951
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.02
r_mcangle_it	2.851
r_mcbond_it	1.963
r_scbond_it	1.954
r_angle_refined_deg	1.664
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.951
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.02
r_mcangle_it	2.851
r_mcbond_it	1.963
r_scbond_it	1.954
r_angle_refined_deg	1.664
r_nbtor_refined	0.324
r_xyhbond_nbd_refined	0.243
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.212
r_symmetry_hbond_refined	0.163
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1252
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.