Experiment: 2QXX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XS1	PDB entry 1XS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	1.9 mg/ml enzyme in 20 mM MgCl2, 5mM dTTP, 50mM HEPES pH 6.8 reservoir solution: 45% PEG 400, 200mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.64	α = 70.75
b = 82.64	β = 70.75
c = 82.64	γ = 70.75

Symmetry
Space Group	R 3 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	ADSC QUANTUM 4		2006-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	19.6	98.1	0.159	15.01		22235	22235	-3	-3	22.025

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	2.1	97.8		0.595	4.5		2973

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1XS1	2	19.58	22234	22234	1112	100	0.164	0.164	0.161	0.16	0.217	0.21	RANDOM	16.975

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]
0.71	-1.08	-1.08	0.71	-1.08	0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.765
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	15.348
r_dihedral_angle_1_deg	5.953
r_scangle_it	3.299
r_mcangle_it	2.995
r_scbond_it	2.434
r_mcbond_it	2.07
r_angle_refined_deg	1.378
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.765
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	15.348
r_dihedral_angle_1_deg	5.953
r_scangle_it	3.299
r_mcangle_it	2.995
r_scbond_it	2.434
r_mcbond_it	2.07
r_angle_refined_deg	1.378
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.25
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.22
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_metal_ion_refined	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2924
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	84

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

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.