2G9F | pdb_00002g9f

Crystal structure of intein-tagged mouse PNGase C-terminal domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	14-16% PEG 8000, 100 mM Tris-HCl, pH 8.5, 120 mM MgCl2 and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.76	α = 90
b = 40.76	β = 90
c = 193.663	γ = 120

Symmetry
Space Group	P 32 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	CCD	ADSC QUANTUM 4		2004-10-02	M	SIRAS

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.0055	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	1.9	50	99.9	0.091	0.091	36.4	9.4	15560	15560			28.9

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	1.9	1.93	98.6		0.622	0.622	3.5	6.7	765

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.9	20	15560	15560	14827	99.84	0.16895	0.16895	0.1668	0.18	0.21265	0.23	RANDOM	36.452

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]
0.12	0.06		0.12		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.767
r_dihedral_angle_4_deg	20.934
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_1_deg	6.948
r_scangle_it	3.232
r_scbond_it	2.301
r_angle_refined_deg	1.413
r_mcangle_it	1.286
r_angle_other_deg	1.194
r_mcbond_it	1.081
r_symmetry_vdw_other	0.259
r_symmetry_hbond_refined	0.234
r_mcbond_other	0.216
r_xyhbond_nbd_refined	0.201
r_nbd_other	0.197
r_nbd_refined	0.194
r_nbtor_refined	0.182
r_symmetry_vdw_refined	0.137
r_chiral_restr	0.094
r_nbtor_other	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1466
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing