2PKQ | pdb_00002pkq

Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RM4	PDB ENTRY 1RM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	2.0-2.5 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.147	α = 90
b = 215.687	β = 102.52
c = 81.469	γ = 90

Symmetry
Space Group	C 1 2 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 4	mirrors	2003-05-03	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4	mirrors	2003-05-03	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2003-10-18	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2
2	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2
3	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.000	ELETTRA	5.2R

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
1,2,3	3.6	91	99.9	0.359	0.359	4.5	13.4	36736	36699	3	-3	15.9

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)
1,2,3	3.6	3.73	99.3		0.694	0.694	1.5		3647

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 (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	PDB ENTRY 1RM4	3.6	90.86	36736	36271	1802	99.9	0.261	0.261	0.24	0.292	0.27	RANDOM	30.9

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]
6.13		-10.38	7		-13.12

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.6
c_improper_angle_d	5.21
c_scangle_it	2.13
c_mcangle_it	1.98
c_angle_deg	1.9
c_scbond_it	1.25
c_mcbond_it	1.11
c_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15477
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	363

Software

Software
Software Name	Purpose
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.