3GNQ | pdb_00003gnq

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	Molecular Dimensions PACT Premier screen condition E1, 25% PEG 3350, 0.2 M NaF with 25% glycerol as cryo-protectant, 33.4 mg/mL protein, crystal ID 201195e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.932	α = 90
b = 173.797	β = 93.29
c = 93.501	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				2008-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97934	APS	24-ID-C

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	2.4	50	99.8	0.096	13.554	3.9		112883

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	2.4	2.49	98.2		0.54	1.74	3.1	11064

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	1obf	THROUGHOUT	2.4	48.84	112829	5649	99.7	0.207	0.204	0.2024	0.263	0.2574	RANDOM	36.647

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]
0.68		0.34	-0.55		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.368
r_dihedral_angle_4_deg	18.287
r_dihedral_angle_3_deg	16.013
r_dihedral_angle_1_deg	6.292
r_scangle_it	2.38
r_scbond_it	1.421
r_angle_refined_deg	1.299
r_mcangle_it	1.099
r_angle_other_deg	0.887
r_mcbond_it	0.587
r_mcbond_other	0.086
r_chiral_restr	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20161
Nucleic Acid Atoms
Solvent Atoms	538
Heterogen Atoms	308

Software

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