2HKI | pdb_00002hki

Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	2-5 % PEG 10,000, 0.4-0.6 M lithium sulphate or 0.8-1 M sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.805	α = 90
b = 120.805	β = 90
c = 159.65	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	IMAGE PLATE	MARRESEARCH	58 CM LONG, PT-COATED,FUSED SILICA, VERTICAL FOCUSMIRROR	2001-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.008	SSRL	BL7-1

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	3	15	99	0.076	0.081	20.1	8.1	12157	12035			80.1

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	3	3.16	100		0.428	0.458	4.1	8.2	1729

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	1RM4	3	15	11522	11522	576	99.94	0.212	0.21236	0.20974	0.28	0.26644	0.33	RANDOM	33.196

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]
-0.82			-0.82		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.016
r_dihedral_angle_3_deg	18.855
r_dihedral_angle_4_deg	14.59
r_dihedral_angle_1_deg	7.11
r_scangle_it	1.698
r_angle_refined_deg	1.472
r_scbond_it	1.074
r_mcangle_it	0.867
r_mcbond_it	0.468
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.016
r_dihedral_angle_3_deg	18.855
r_dihedral_angle_4_deg	14.59
r_dihedral_angle_1_deg	7.11
r_scangle_it	1.698
r_angle_refined_deg	1.472
r_scbond_it	1.074
r_mcangle_it	0.867
r_mcbond_it	0.468
r_nbtor_refined	0.315
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2529
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	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.