Experiment: 3D23

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	sodium acetate, pH 6.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	58.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.77	α = 90
b = 91.77	β = 90
c = 187.914	γ = 90

Symmetry
Space Group	P 41

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.9998	Photon Factory	BL-5A

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	2.5	100	99.8	0.11	16	5		108501

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	2.5	2.6	98.1			5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.5	50	52904	2654	98.64	0.232	0.229	0.285	RANDOM	39.016

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]
1.06			1.06		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.206
r_dihedral_angle_3_deg	19.354
r_dihedral_angle_4_deg	16.687
r_dihedral_angle_1_deg	8.822
r_scangle_it	4.374
r_scbond_it	2.962
r_angle_refined_deg	2.083
r_mcangle_it	1.949
r_mcbond_it	1.198
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.206
r_dihedral_angle_3_deg	19.354
r_dihedral_angle_4_deg	16.687
r_dihedral_angle_1_deg	8.822
r_scangle_it	4.374
r_scbond_it	2.962
r_angle_refined_deg	2.083
r_mcangle_it	1.949
r_mcbond_it	1.198
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.286
r_nbd_refined	0.249
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.135
r_symmetry_hbond_refined	0.127
r_bond_refined_d	0.022
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9363
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.