2I74

Crystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with mannopentaose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	19 % PEG 4000, 11.5 % Isopropanol, 0.1 M Tris-HCl, pH 7.5, 0.2 M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.706	α = 90
b = 41.646	β = 94.89
c = 94.9	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	CCD	ADSC QUANTUM 315		2006-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.97950	NSLS	X25

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	1.75	50	99.9	0.087	0.087	20	5.5	35889	35889			16.6

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	1.75	1.81	100		0.441	0.441	3.3	5.5	3565

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2G9F	1.75	20	2	35889	35851	1856	99.67	0.174	0.172	0.208	RANDOM	13.838

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]
1.05		0.44	-0.59		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.553
r_dihedral_angle_4_deg	14.186
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	6.591
r_scangle_it	3.24
r_scbond_it	2.309
r_angle_other_deg	1.668
r_angle_refined_deg	1.543
r_mcangle_it	1.294
r_mcbond_it	1.127
r_symmetry_vdw_refined	0.401
r_symmetry_vdw_other	0.346
r_mcbond_other	0.251
r_nbd_other	0.234
r_symmetry_hbond_refined	0.221
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.215
r_nbtor_refined	0.181
r_chiral_restr	0.125
r_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2915
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	132

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing