Experiment: 2Z5P

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.79	α = 90
b = 180.79	β = 90
c = 180.79	γ = 90

Symmetry
Space Group	F 4 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 315		2006-03-03	M	SINGLE WAVELENGTH
2	1	100	CCD	ADSC QUANTUM 315		2006-03-03

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.5086	SPring-8	BL41XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.4639	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	1.65	50	100	0.085	40	21.5		30995		-3	15.581

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	1.65	1.693	100		0.298	14.1	22.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1DAT	1.65	34.79	29369	1578	99.93	0.16959	0.1686	0.18788	RANDOM	17.148

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.068
r_dihedral_angle_4_deg	16.13
r_dihedral_angle_3_deg	12.914
r_dihedral_angle_1_deg	4.241
r_sphericity_free	2.996
r_scangle_it	2.949
r_scbond_it	1.934
r_angle_refined_deg	1.144
r_mcangle_it	1.021
r_mcbond_it	0.683

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.068
r_dihedral_angle_4_deg	16.13
r_dihedral_angle_3_deg	12.914
r_dihedral_angle_1_deg	4.241
r_sphericity_free	2.996
r_scangle_it	2.949
r_scbond_it	1.934
r_angle_refined_deg	1.144
r_mcangle_it	1.021
r_mcbond_it	0.683
r_nbtor_refined	0.303
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.21
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
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 R01GM133198.