5FH3 | pdb_00005fh3

The structure of rat cytosolic PEPCK variant E89A in complex with oxalic acid and GTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DT4

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
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.699	α = 90
b = 119.313	β = 107.95
c = 60.821	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 315r		2011-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97	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	1.6	100	98.7	0.069	16.2	5.9		80122

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	1.6	1.66	91.5		0.308		5.2	7417

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	3DT4	1.6	59.66	76005	4009	98.53	0.2068	0.2048	0.21	0.2428	0.25	RANDOM	22.103

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.782
r_dihedral_angle_4_deg	15.509
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_1_deg	6.767
r_mcangle_it	2.288
r_angle_refined_deg	1.436
r_mcbond_it	1.377
r_mcbond_other	1.377
r_angle_other_deg	0.883
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.782
r_dihedral_angle_4_deg	15.509
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_1_deg	6.767
r_mcangle_it	2.288
r_angle_refined_deg	1.436
r_mcbond_it	1.377
r_mcbond_other	1.377
r_angle_other_deg	0.883
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4802
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	74

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.