2PAN | pdb_00002pan

Crystal structure of E. coli glyoxylate carboligase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	294	2-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) were mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M NaCl, 40 mM DTT), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294.K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.18	α = 90
b = 188.18	β = 90
c = 249.4	γ = 90

Symmetry
Space Group	P 41 21 2

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	BENT CRYSTAL	2004-12-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97897, 0.97946, 0.93929	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	50	99.2	0.101	0.089	9.43	4.4		122672		-3	37.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	93.1		0.347	0.28	2.76	2.21

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	MAD	THROUGHOUT	2.7	20	122207	2453	99.9	0.22	0.219	0.22	0.253	0.26	RANDOM	27.79

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]
-0.09			-0.09		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.25
r_dihedral_angle_4_deg	17.681
r_dihedral_angle_3_deg	14.993
r_dihedral_angle_1_deg	5.916
r_scangle_it	1.463
r_angle_refined_deg	1.229
r_scbond_it	1.024
r_angle_other_deg	0.79
r_mcbond_it	0.524
r_mcangle_it	0.504
r_symmetry_vdw_other	0.198
r_symmetry_vdw_refined	0.19
r_nbd_refined	0.184
r_nbtor_refined	0.17
r_nbd_other	0.169
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.127
r_nbtor_other	0.081
r_mcbond_other	0.065
r_chiral_restr	0.064
r_xyhbond_nbd_other	0.02
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
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	27180
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	548

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction