2WZD

The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with ADP, 3PG and aluminium trifluoride

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C39	PDB ENTRY 3C39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		22% PEG2000MME, 0.1M BIS/TRIS PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.38	α = 90
b = 91.59	β = 90
c = 108.48	γ = 90

Symmetry
Space Group	P 21 21 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 CCD	GE211	2009-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		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	1.56	20	98	0.06	10.9	2.7		55495		3	14.5

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	1.56	1.64	95.9		0.28	3.7	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3C39	1.56	20	52652	2800	97.71	0.16815	0.16634	0.20181	RANDOM	5.368

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]
-0.37			0.95		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.543
r_dihedral_angle_4_deg	18.555
r_dihedral_angle_3_deg	13.274
r_dihedral_angle_1_deg	7.384
r_scangle_it	3.644
r_scbond_it	2.279
r_angle_refined_deg	1.646
r_mcangle_it	1.352
r_angle_other_deg	0.942
r_mcbond_it	0.811
r_mcbond_other	0.267
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	44

Software

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