Experiment: 3B4Y

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		an in-house apo structure (itself solved by Se-MAD)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	1.4M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.078	α = 90
b = 89.907	β = 90
c = 80.146	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 345 mm plate	osmic	2007-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.95	25.18	96.7	0.114	17.6	9.8	47109	47019

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	1.95	2.06	92.6		0.484	1.2	2	13127

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	an in-house apo structure (itself solved by Se-MAD)	1.95	24.65	44565	44565	2330	96.43	0.19385	0.19385	0.19174	0.2	0.23434	0.21	RANDOM	20.083

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]
-0.63			0.46		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	16.448
r_dihedral_angle_3_deg	15.301
r_dihedral_angle_1_deg	6.494
r_scangle_it	2.587
r_scbond_it	2.072
r_angle_refined_deg	1.646
r_mcangle_it	1.21
r_mcbond_it	0.752
r_symmetry_hbond_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	16.448
r_dihedral_angle_3_deg	15.301
r_dihedral_angle_1_deg	6.494
r_scangle_it	2.587
r_scbond_it	2.072
r_angle_refined_deg	1.646
r_mcangle_it	1.21
r_mcbond_it	0.752
r_symmetry_hbond_refined	0.307
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.116
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5140
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	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.