7BEX | pdb_00007bex

Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeuni - ADP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BEW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	0.1M Sodium Acetate, 2.0 M Ammonium Sulfate,

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.25	α = 90
b = 90.25	β = 90
c = 223.39	γ = 90

Symmetry
Space Group	I 41 2 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	RIGAKU	varimax HF	2013-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.05	83.67	91.3	0.13	9.9	10.9		29280

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	2.05	2.11	94.9		0.32		6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7BEW	2.054	30.105	29252	1437	99.898	0.156	0.1546	0.17	0.1905	0.2	random	17.297

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]
-0.007			-0.007		0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.285
r_dihedral_angle_4_deg	18.219
r_dihedral_angle_3_deg	12.756
r_dihedral_angle_1_deg	7.513
r_lrange_it	5.817
r_lrange_other	5.774
r_scangle_it	4.376
r_scangle_other	4.375
r_scbond_it	2.981
r_scbond_other	2.98
r_mcangle_other	2.494
r_mcangle_it	2.493
r_angle_refined_deg	1.709
r_mcbond_it	1.619
r_mcbond_other	1.607
r_angle_other_deg	1.422
r_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.187
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.163
r_xyhbond_nbd_refined	0.153
r_nbd_other	0.144
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2519
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
pointless	data scaling
PHASER	phasing