2VGB

HUMAN ERYTHROCYTE PYRUVATE KINASE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	RECOMBINANT WILD-TYPE RPK WAS CRYSTALLIZED USING THE VAPOR DIFFUSION METHOD AT 22 C. WELL SOLUTIONS CONSISTED OF 50 MM MES/KOH, PH 6.4, 10 MM MNSO4, AND 10-14% W/V PEG8000. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 12 MG/ML PROTEIN IN 50 MM KCL, 5 MM FBP, 5 MM PHOSPHOGLYCOLATE, 20 MM POTASSIUM PHOSPHATE, PH 7.0, AND WELL SOLUTIONS.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.413	α = 90
b = 172.058	β = 92.46
c = 85.512	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	IMAGE PLATE				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF		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	2.7	20	95.9	0.08	13.4	2.1		55091

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	2.7	2.7	86.5		0.24	2.4	2.1

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 1PKN	2.73	20	52174	2780	96.3	0.229	0.227	0.271	RANDOM	40.86

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]
-0.14		0.12	0.2		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.011
r_dihedral_angle_4_deg	23.116
r_dihedral_angle_3_deg	20.809
r_dihedral_angle_1_deg	5.423
r_scangle_it	2.564
r_scbond_it	1.546
r_angle_refined_deg	1.513
r_mcangle_it	0.785
r_symmetry_vdw_refined	0.54
r_mcbond_it	0.399
r_nbtor_refined	0.322
r_symmetry_hbond_refined	0.315
r_nbd_refined	0.257
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	15423
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing