9FL1 | pdb_00009fl1

Apo Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GD1	monomer with ligands removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	300	17% w/v PEG8000, 100mM Hepes, 12mg/ml protein

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.16	α = 90
b = 100.617	β = 93.696
c = 97.792	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	CCD	ADSC QUANTUM 4r		2003-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.74	95.4	99	0.161	19	2.1		147140

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	1.74	1.82	99		0.534	2.2	2.1

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	1.74	95.346	147140	7374	99.053	0.152	0.1498	0.1635	0.1995	0.2077	27.35

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]
1.598		3.3	-0.82		-1.194

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.766
r_lrange_other	19.002
r_dihedral_angle_6_deg	15.892
r_scangle_it	12.955
r_scangle_other	12.954
r_dihedral_angle_3_deg	12.263
r_mcangle_it	10.251
r_mcangle_other	10.251
r_scbond_it	8.868
r_scbond_other	8.86
r_dihedral_angle_2_deg	7.696
r_mcbond_it	7.273
r_mcbond_other	7.271
r_dihedral_angle_1_deg	7.072
r_rigid_bond_restr	4.269
r_angle_refined_deg	1.642
r_angle_other_deg	0.57
r_nbd_refined	0.217
r_symmetry_nbd_other	0.206
r_nbd_other	0.187
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.145
r_metal_ion_refined	0.1
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.008
r_chiral_restr_other	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9706
Nucleic Acid Atoms
Solvent Atoms	1006
Heterogen Atoms	75

Software

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