2FAF | pdb_00002faf

The structure of chicken mitochondrial PEPCK.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KHG	PDB Entry 1KHG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	19% PEG 6000, HEPES pH 7.4, n-octanoyl sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.807	α = 90
b = 47.737	β = 111.31
c = 127.205	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 4		2004-05-15	M	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	1.7	50	90.9	0.054		4.3		123916

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	1.7	1.76	86.3		0.541		3.9	11661

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	PDB Entry 1KHG	1.7	34.08	123906	123906	6219	90.59	0.162	0.162	0.161	0.1595	0.191	0.1891	RANDOM	24.702

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]
-0.04		-0.03	0.06		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.655
r_dihedral_angle_4_deg	16.796
r_dihedral_angle_3_deg	12.77
r_dihedral_angle_1_deg	5.845
r_scangle_it	2.731
r_scbond_it	1.753
r_angle_refined_deg	1.332
r_mcangle_it	1.058
r_mcbond_it	0.717
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9306
Nucleic Acid Atoms
Solvent Atoms	980
Heterogen Atoms	65

Software

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