Experiment: 6HMM

POLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00013907

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	Mix purified protein in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT at 7.5 mg/mL with a precipitant consisting of 28% PEG-3350, 0.2 M magnesium chloride, 0.1 M PCTP (0.04 M sodium propionate, 0.02 M sodium cacodylate, 0.04 M Bis-Tris propane) pH 7.5.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.081	α = 90
b = 90.367	β = 90
c = 95.41	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	RIGAKU SATURN 944	Rigaku VariMaxHF	2010-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54

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	1.89	95.41	95.7	0.079	12	4.7		45150			26.42

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	1.89	1.99	78.3		0.457	2	2.3	2509

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4A0D	1.9	27.8	44100	2246	95.7	0.2041	0.2012	0.2112	0.2588	0.2704	RANDOM	29.59

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]
4.0857			-1.0638		-3.0219

RMS Deviations
Key	Refinement Restraint Deviation
OTHER TORSION ANGLES	16.86
PEPTIDE OMEGA TORSION ANGLES	3.21
BOND ANGLES	1.06
BOND LENGTHS	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4062
Nucleic Acid Atoms
Solvent Atoms	525
Heterogen Atoms	55

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BUSTER	refinement
PHASER	phasing