Experiment: 4B5S

Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with pyruvate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5J	PDB ENTRY 2V5J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.5 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% GLYCEROL, 2 MM COCL2 PH 5

Crystal Properties
Matthews coefficient	Solvent content
3.85	67.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.74	α = 90
b = 151.74	β = 90
c = 151.74	γ = 90

Symmetry
Space Group	P 21 3

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 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

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	1.68	45.7	99.9	0.02	19.2	21.4		131767		1	25.54

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	1.68	1.72	100		0.41	2	19.15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2V5J	1.68	40.554	1.34	131756	9871	99.95	0.1536	0.1515	0.1567	0.1789	0.1831	24.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.195
f_angle_d	1.647
f_chiral_restr	0.103
f_bond_d	0.018
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3800
Nucleic Acid Atoms
Solvent Atoms	1091
Heterogen Atoms	48

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	phasing