2RKA | pdb_00002rka

The Structure of rat cytosolic PEPCK in complex with phosphoglycolate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.67	α = 90
b = 119.66	β = 108.9
c = 90.867	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	118	IMAGE PLATE	RIGAKU RAXIS IV++	BLUE OSMIC Confocal MIRRORS	2007-05-29		SINGLE WAVELENGTH

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

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	1.95	100	96.5	0.105	9.5	6.8		86353

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	1.95	2.02	94.6		0.705		6.3	8410

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	1.95	29.92	86305	4327	96.36	0.185	0.183	0.18	0.222	0.22	RANDOM	19.115

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]
-0.15		0.15	-0.12		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.064
r_dihedral_angle_4_deg	16.704
r_dihedral_angle_3_deg	14.682
r_dihedral_angle_1_deg	5.625
r_scangle_it	1.881
r_scbond_it	1.156
r_angle_refined_deg	1.125
r_mcangle_it	0.706
r_mcbond_it	0.383
r_nbtor_refined	0.302
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.182
r_symmetry_vdw_refined	0.162
r_xyhbond_nbd_refined	0.134
r_metal_ion_refined	0.105
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9636
Nucleic Acid Atoms
Solvent Atoms	1018
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction