Experiment: 2O03

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.3 M ammonium phosphate, 14% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 51.6	β = 90
c = 133.4	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	MARMOSAIC 225 mm CCD		2006-04-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2006-04-29	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.28087	SLS	X06SA
2	SYNCHROTRON	SLS BEAMLINE X06SA	1.28358, 1.28441, 1.26924	SLS	X06SA

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	2.69	40	97.8	0.069	0.107	18.85	16.76	5464	5344		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.69	2.85	92.8		0.31	0.64	4.4	16.7	775

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.699	33.69	5344	268	100	0.23	0.23	0.239	RANDOM	53.712

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]
1.92			1.92		-3.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.011
r_dihedral_angle_3_deg	18.209
r_dihedral_angle_4_deg	16.251
r_dihedral_angle_1_deg	6.662
r_scangle_it	2.707
r_scbond_it	2.26
r_angle_refined_deg	1.389
r_mcangle_it	0.926
r_mcbond_it	0.526
r_nbtor_refined	0.286

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.011
r_dihedral_angle_3_deg	18.209
r_dihedral_angle_4_deg	16.251
r_dihedral_angle_1_deg	6.662
r_scangle_it	2.707
r_scbond_it	2.26
r_angle_refined_deg	1.389
r_mcangle_it	0.926
r_mcbond_it	0.526
r_nbtor_refined	0.286
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	954
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
GCLIENT	data collection
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building

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.