2IBP | pdb_00002ibp

Crystal Structure of Citrate Synthase from Pyrobaculum aerophilum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VGP	PDB ENTRY 1VGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	297	20% PEG 8000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Magnesium acetate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.418	α = 90
b = 89.803	β = 90
c = 146.331	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	Mirrors	2005-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	76.47	95.5	0.085	21.2	6.9	107121	107121			22.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	90.2		0.686	3.2	5.8	9959

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 1VGP	1.6	76.47	100651	100651	5286	94.34	0.15929	0.15929	0.15769	0.17	0.18975	0.2	RANDOM	12.828

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			0.28		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.68
r_dihedral_angle_4_deg	11.106
r_dihedral_angle_3_deg	9.834
r_scangle_it	7.403
r_scbond_it	5.36
r_mcbond_it	4.306
r_mcangle_it	4.306
r_dihedral_angle_1_deg	3.303
r_angle_refined_deg	1.227
r_mcbond_other	0.968
r_angle_other_deg	0.81
r_symmetry_vdw_other	0.282
r_nbd_refined	0.219
r_nbd_other	0.205
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.193
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.105
r_chiral_restr	0.093
r_nbtor_other	0.088
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6528
Nucleic Acid Atoms
Solvent Atoms	808
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
BOS	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing