2QEY | pdb_00002qey

Rat cytosolic PEPCK in complex with GTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QEW

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, 10mM MnCl2, 10mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.713	α = 90
b = 118.851	β = 108.84
c = 60.704	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	IMAGE PLATE	RIGAKU RAXIS IV++	blue osmic confocal	2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	1.9	100	89.3	0.117	10.5	6.7	42128	42128	2	2

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	1.9	1.97	46.1		0.575		3.8	2168

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2QEW	1.9	32.62	42102	42102	2134	89.16	0.195	0.195	0.193	0.1969	0.229	0.2225	RANDOM	18.023

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]
0.54		0.29	-0.39		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.108
r_dihedral_angle_4_deg	14.458
r_dihedral_angle_3_deg	13.963
r_dihedral_angle_1_deg	5.126
r_angle_refined_deg	1.01
r_scangle_it	0.911
r_scbond_it	0.572
r_mcangle_it	0.399
r_nbtor_refined	0.299
r_mcbond_it	0.217
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.148
r_symmetry_hbond_refined	0.107
r_xyhbond_nbd_refined	0.105
r_metal_ion_refined	0.093
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4801
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	40

Software

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