Experiment: 1X25

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QD9	PDB ENTRY 1QD9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3	293	PEG 10000, Bis-Tris, ammonium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.33	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.98	α = 90
b = 54.98	β = 90
c = 221.557	γ = 120

Symmetry
Space Group	H 3

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 VII		2004-09-01	M	SINGLE WAVELENGTH

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

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	22.051	99.8	0.061	0.055	9.8	6.2	16882	16882		5.1	17.336

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	2.11	99.8		0.151	0.137	5.1	5.9	182

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 1QD9	2	19.03	16877	16877	852	99.82	0.14787	0.14787	0.14578	0.15	0.18799	0.19	RANDOM	18.36

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]
0.27	0.14		0.27		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.343
r_scangle_it	4.987
r_scbond_it	3.028
r_mcangle_it	1.79
r_angle_refined_deg	1.488
r_mcbond_it	1.005
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.343
r_scangle_it	4.987
r_scbond_it	3.028
r_mcangle_it	1.79
r_angle_refined_deg	1.488
r_mcbond_it	1.005
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.114
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1979
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CCP4	data scaling
MOLREP	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.