5FH4 | pdb_00005fh4

The structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and GTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DT7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	25% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.59	α = 90
b = 118.809	β = 109.3
c = 60.508	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 315		2011-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.9	SSRL	BL7-1

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	1.49	100	99.9	0.088	13	6.1		95906

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	1.5	1.55	99.9		0.512		5.9	9625

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	3DT7	1.49	34.34	90947	4787	99.1	0.2056	0.2044	0.21	0.2286	0.23	RANDOM	23.33

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]
-0.39		-0.16	-0.01		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.177
r_dihedral_angle_4_deg	16.611
r_dihedral_angle_3_deg	12.763
r_dihedral_angle_1_deg	6.398
r_angle_refined_deg	1.621
r_angle_other_deg	0.968
r_mcangle_it	0.374
r_mcbond_it	0.209
r_mcbond_other	0.209
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.177
r_dihedral_angle_4_deg	16.611
r_dihedral_angle_3_deg	12.763
r_dihedral_angle_1_deg	6.398
r_angle_refined_deg	1.621
r_angle_other_deg	0.968
r_mcangle_it	0.374
r_mcbond_it	0.209
r_mcbond_other	0.209
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4811
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	54

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	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.