Experiment: 2F8V

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YA5	PDB ENTRY 1YA5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.45	298	PEG35000, LITHIUM SULPHATE, ACETATE BUFFER, pH 4.45, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.513	α = 90
b = 46.885	β = 98.3
c = 128.033	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARRESEARCH		2002-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8117	EMBL/DESY, HAMBURG	X11

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	2.75	23.9	96.1	0.101			33692	33692	1	1	60

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.8	79.9

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 1YA5	2.75	23.9	32562	32562	1063	100	0.2655	0.26734	0.26671	0.26	0.28733	0.28	RANDOM	22.944

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]
7.18		-5.44	-7.85		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.142
r_dihedral_angle_4_deg	25.458
r_dihedral_angle_3_deg	20.342
r_dihedral_angle_1_deg	4.825
r_scangle_it	3.103
r_scbond_it	2.614
r_mcangle_it	1.996
r_mcbond_it	1.604
r_angle_refined_deg	1.403
r_symmetry_vdw_refined	0.419

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.142
r_dihedral_angle_4_deg	25.458
r_dihedral_angle_3_deg	20.342
r_dihedral_angle_1_deg	4.825
r_scangle_it	3.103
r_scbond_it	2.614
r_mcangle_it	1.996
r_mcbond_it	1.604
r_angle_refined_deg	1.403
r_symmetry_vdw_refined	0.419
r_nbtor_refined	0.34
r_nbd_refined	0.288
r_xyhbond_nbd_refined	0.203
r_symmetry_hbond_refined	0.168
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7280
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.