2F4M | pdb_00002f4m

The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	291	0.1 M Tris-HCl, pH 8.5, 28-32% PEG4000, 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.225	α = 90
b = 52.297	β = 115.33
c = 82.548	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		2005-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	50	95.9	0.051	15.5	4.5		31216			42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.91	20.9		0.4	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MIR	THROUGHOUT	1.85	20	2	40360	29636	1579	96	0.189	0.186	0.1941	0.239	0.2451	RANDOM	42.62

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]
1.55		0.23	1.07		-2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.561
r_dihedral_angle_4_deg	21.925
r_dihedral_angle_3_deg	17.37
r_dihedral_angle_1_deg	6.909
r_scangle_it	2.793
r_scbond_it	2.009
r_angle_refined_deg	1.547
r_mcangle_it	1.214
r_mcbond_it	1.01
r_angle_other_deg	0.915
r_symmetry_hbond_refined	0.334
r_xyhbond_nbd_refined	0.259
r_mcbond_other	0.249
r_nbd_refined	0.214
r_nbd_other	0.196
r_nbtor_refined	0.173
r_symmetry_vdw_other	0.168
r_symmetry_vdw_refined	0.153
r_chiral_restr	0.093
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2953
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing