9FOB | pdb_00009fob

Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori in Complex with NAPD (Holo)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GD1	one monomer (O chain +NAD)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293	100mM Tris, 36% v/v methanol, 1mM NADP

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.938	α = 90
b = 116.938	β = 90
c = 95.474	γ = 120

Symmetry
Space Group	P 32

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 4r		2007-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2.6	69.5	96.8	0.045	17.9	3.6		43460

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	2.6	2.74	88.3		0.193	5.7	2.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	44.774	43438	2077	96.826	0.178	0.1746	0.1802	0.2414	0.2483	55.246

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]
0.809	0.404		0.809		-2.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.805
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_2_deg	9.769
r_lrange_other	8.257
r_lrange_it	8.256
r_dihedral_angle_1_deg	7.166
r_scangle_it	6.603
r_scangle_other	6.603
r_mcangle_it	5.978
r_mcangle_other	5.978
r_scbond_it	4.49
r_scbond_other	4.485
r_mcbond_it	4.236
r_mcbond_other	4.233
r_dihedral_angle_other_2_deg	2.444
r_angle_refined_deg	1.524
r_angle_other_deg	0.492
r_nbd_refined	0.22
r_symmetry_nbd_other	0.204
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.177
r_nbtor_refined	0.17
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10357
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing