Experiment: 4DPZ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DOT	PDB ENTRY 4DOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	1.1 ammonium tartrate dibasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.738	α = 90
b = 37.078	β = 113.38
c = 45.423	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	ADSC QUANTUM 315r		2011-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C

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	1.25	30	98	0.047	22		34298	34298		-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	1.25	1.29	99.9		0.285	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DOT	1.25	20.82	32554	32554	1726	97.28	0.15147	0.15147	0.14999	0.17884	RANDOM	21.27

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]
-0.35		0.96	-1.09		2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.48
r_dihedral_angle_2_deg	24.824
r_sphericity_bonded	20.166
r_rigid_bond_restr	13.629
r_dihedral_angle_3_deg	12.291
r_dihedral_angle_4_deg	11.668
r_dihedral_angle_1_deg	5.898
r_angle_refined_deg	1.657
r_angle_other_deg	1.052
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.48
r_dihedral_angle_2_deg	24.824
r_sphericity_bonded	20.166
r_rigid_bond_restr	13.629
r_dihedral_angle_3_deg	12.291
r_dihedral_angle_4_deg	11.668
r_dihedral_angle_1_deg	5.898
r_angle_refined_deg	1.657
r_angle_other_deg	1.052
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	854
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.