3Q1G | pdb_00003q1g

Crystal Structure of BoxB crystallized with PEG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PF7	pdb entry 3PF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	13% PEG 4000 0.1M sodium acetate, pH 4.6 0.1M Li2SO4 18% glycerol 5 mM benzoyl-CoA 0.1 mg/ml BoxA 0.1 M KCl 10 mM Pipes, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.66	α = 90
b = 76.77	β = 109.43
c = 147.83	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	PSI PILATUS 6M		2010-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	43.7	99	0.131	0.113	8.56		77107	76352

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	96.3

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 (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 3PF7	2.5	43.7	72478	3824	99.03	0.20735	0.2059	0.2	0.23498	0.23	RANDOM	46.457

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]
-1.08		0.15	1.73		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.377
r_dihedral_angle_4_deg	21.373
r_dihedral_angle_3_deg	14.752
r_dihedral_angle_1_deg	5.637
r_scangle_it	3.307
r_scbond_it	2.209
r_angle_refined_deg	1.317
r_mcangle_it	1.165
r_angle_other_deg	0.94
r_mcbond_it	0.571

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.377
r_dihedral_angle_4_deg	21.373
r_dihedral_angle_3_deg	14.752
r_dihedral_angle_1_deg	5.637
r_scangle_it	3.307
r_scbond_it	2.209
r_angle_refined_deg	1.317
r_mcangle_it	1.165
r_angle_other_deg	0.94
r_mcbond_it	0.571
r_mcbond_other	0.103
r_chiral_restr	0.072
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15298
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	36

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	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.