3PMS

Recombinant peptide: N-glycanase F (PNGase F)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	295.15	25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.96	α = 90
b = 90.56	β = 112.3
c = 48.81	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	120	IMAGE PLATE	RIGAKU RAXIS IV++		2009-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.542

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	1.57	40.41	96.6	0.057			43449	41972

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PGS	1.57	34.02	41972	2256	100	0.1524	0.151	0.1778	RANDOM	18.3064

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]
1.11		-0.4	-0.92		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.01
r_dihedral_angle_3_deg	13.677
r_dihedral_angle_4_deg	10.833
r_dihedral_angle_1_deg	7.08
r_scangle_it	5.044
r_scbond_it	3.282
r_mcangle_it	2.475
r_angle_refined_deg	1.821
r_mcbond_it	1.608
r_angle_other_deg	0.927
r_mcbond_other	0.535
r_chiral_restr	0.122
r_bond_refined_d	0.02
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2452
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	78

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XSCALE	data scaling