Experiment: 1PT5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PT7	apo-enzyme

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	PEG600, cacodylate, acetylCoA, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.16	70.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.882	α = 90
b = 146.882	β = 90
c = 129.515	γ = 120

Symmetry
Space Group	P 62

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 4		2002-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9330	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	20	99	0.078	7	6.5	105732	105732	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11	97.5		0.265

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	apo-enzyme	2	20	2	105732	96936	8795	99.08	0.1592	0.1592	0.15769	0.17598	RANDOM	23.857

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]
-1.38	-0.69		-1.38		2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.367
r_scangle_it	4.373
r_scbond_it	2.644
r_mcangle_it	1.535
r_angle_refined_deg	1.498
r_mcbond_it	0.785
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.367
r_scangle_it	4.373
r_scbond_it	2.644
r_mcangle_it	1.535
r_angle_refined_deg	1.498
r_mcbond_it	0.785
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6432
Nucleic Acid Atoms
Solvent Atoms	617
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	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.