2HPJ

Crystal structure of the PUB domain of mouse PNGase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	281	18-22% PEG 5000 MME and 14-18% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.641	α = 90
b = 52.042	β = 115.25
c = 34.946	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU RAXIS IV		2006-03-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2006-03-29	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X26C	1.0074	NSLS	X26C

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
1,2	1.7	50	95	0.055	0.055	23.9	4.08		11390	2	2	16.8

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)
1,2	1.7	1.76	56.8		0.106	0.106	6.6	1.9	682

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	SIRAS	THROUGHOUT	1.7	20	2	2	10843	11387	544	94.77	0.149	0.148	0.147	0.16	0.177	0.19	RANDOM	11.93

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]
0.94		0.03	0.11		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.706
r_dihedral_angle_4_deg	17.56
r_dihedral_angle_3_deg	11.856
r_dihedral_angle_1_deg	5.33
r_scangle_it	3.522
r_scbond_it	2.523
r_angle_refined_deg	1.529
r_mcangle_it	1.378
r_mcbond_it	1.277
r_angle_other_deg	0.913
r_symmetry_vdw_other	0.283
r_mcbond_other	0.282
r_nbd_refined	0.226
r_nbd_other	0.187
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.181
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.1
r_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	779
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction