3QV1 | pdb_00003qv1

Crystal structure of the binary complex of photosyntetic A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with cp12-2, both from Arabidopsis thaliana.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	15% (w/v) PEG 4K, 0.6 M NaCl, 1 mM NAD and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.67	α = 90
b = 245.99	β = 90
c = 138.66	γ = 90

Symmetry
Space Group	C 2 2 21

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		2007-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	34.2	99.2	0.139	0.139	5.9	3.3	168053	163587	3	3	23.6

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	2.08	98.2		0.716	0.716	1.3	3.2	24070

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	3K2B	2	34.2	153928	153928	8137	99.04	0.22776	0.22776	0.22537	0.23	0.27243	0.28	RANDOM	30.638

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]
-2.31			-0.67		2.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.578
r_dihedral_angle_4_deg	19.599
r_dihedral_angle_3_deg	18.292
r_dihedral_angle_1_deg	7.094
r_mcangle_it	1.801
r_angle_refined_deg	1.737
r_scangle_it	1.595
r_mcbond_it	1.47
r_scbond_it	1.107
r_angle_other_deg	0.824
r_symmetry_vdw_other	0.297
r_symmetry_hbond_refined	0.284
r_mcbond_other	0.28
r_symmetry_vdw_refined	0.272
r_nbd_other	0.226
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.185
r_nbtor_other	0.097
r_chiral_restr	0.095
r_xyhbond_nbd_other	0.065
r_symmetry_hbond_other	0.064
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_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	15827
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	299

Software

Software
Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling