Experiment: 2QD0

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris-HCl, 18% PEG 3350 , 200 mM KI., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	7.4	293	100 mM Tris-HCl, 30% PEG 2000 ,100 mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.838	α = 90
b = 59.139	β = 90
c = 65.971	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2006-05-19	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315		2006-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418
2	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.8	50	95.2	0.045	15.2	6.4		15523		-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	1.8	1.83	76.8		0.216		5.4	616

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	SAD	THROUGHOUT	1.81	21.92	14902	739	91.62	0.166	0.164	0.193	RANDOM	49.944

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]
5.12			-3.93		-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.065
r_dihedral_angle_3_deg	14.192
r_dihedral_angle_4_deg	6.664
r_dihedral_angle_1_deg	5.679
r_scangle_it	2.877
r_scbond_it	1.939
r_angle_refined_deg	1.888
r_mcangle_it	1.214
r_mcbond_it	0.803
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.065
r_dihedral_angle_3_deg	14.192
r_dihedral_angle_4_deg	6.664
r_dihedral_angle_1_deg	5.679
r_scangle_it	2.877
r_scbond_it	1.939
r_angle_refined_deg	1.888
r_mcangle_it	1.214
r_mcbond_it	0.803
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.135
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1074
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	phasing
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	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.