Experiment: 2R94

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W3N	PDB entry 1W3N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	HEPES/KOH, pH 7, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.76	α = 90
b = 149.76	β = 90
c = 173.47	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	100	CCD	MARMOSAIC 225 mm CCD		2006-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.98	SLS	X10SA

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	49.95	100	0.086	0.107	14.48	9.8	100116	100096		3	35

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)
	2.2	2.5	100		0.23	0.497	5.02	10	100096

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		THROUGHOUT	PDB entry 1W3N	2.2	47.95	100094	5005	100	0.188	0.18535	0.18	0.225	0.22	RANDOM	34.523

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]
-0.91			-0.91		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.328
r_dihedral_angle_4_deg	21.601
r_dihedral_angle_3_deg	16.097
r_dihedral_angle_1_deg	10.175
r_scangle_it	3.044
r_mcangle_it	2.717
r_scbond_it	1.936
r_angle_refined_deg	1.801
r_mcbond_it	1.717
r_symmetry_hbond_refined	0.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.328
r_dihedral_angle_4_deg	21.601
r_dihedral_angle_3_deg	16.097
r_dihedral_angle_1_deg	10.175
r_scangle_it	3.044
r_mcangle_it	2.717
r_scbond_it	1.936
r_angle_refined_deg	1.801
r_mcbond_it	1.717
r_symmetry_hbond_refined	0.762
r_nbtor_refined	0.334
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8660
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	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.