3DT4 | pdb_00003dt4

The structure of rat cytosolic PEPCK in complex with oxalate and GTP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop vapor diffusion	7.4	298	12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, hanging drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.454	α = 90
b = 119.759	β = 96.7
c = 87.3	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2007-12-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9	SSRL	BL11-1

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	1.45	100	99.8	0.08	9.5	7.1		217132

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	1.45	1.5	98		0.717		5.7	21289

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.45	30.02	217074	10901	99.76	0.176	0.175	0.1901	0.203	0.2142	RANDOM	11.462

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]
-0.1		-0.03	-0.04		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.066
r_dihedral_angle_4_deg	15.486
r_dihedral_angle_3_deg	13.63
r_dihedral_angle_1_deg	6.038
r_scangle_it	3.918
r_scbond_it	2.471
r_angle_refined_deg	1.601
r_mcangle_it	1.538
r_mcbond_it	0.915
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9731
Nucleic Acid Atoms
Solvent Atoms	1469
Heterogen Atoms	92

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling