1X3Z | pdb_00001x3z

Structure of a peptide:N-glycanase-Rad23 complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
6.7	81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.801	α = 90
b = 128.801	β = 90
c = 128.376	γ = 120

Symmetry
Space Group	P 31 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	93	CCD	KODAK		2005-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0721	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	30	97.4			30868	30868	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	91

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	20	28388	28388	1471	97.47	0.23737	0.23737	0.23572	0.2377	0.2701	0.2327	RANDOM	63.515

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]
3.34	1.67		3.34		-5.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.756
r_dihedral_angle_3_deg	24.366
r_dihedral_angle_4_deg	22.802
r_dihedral_angle_1_deg	7.14
r_rigid_bond_restr	4.222
r_sphericity_free	3.905
r_scbond_it	3.454
r_scangle_it	3.281
r_mcangle_it	1.891
r_sphericity_bonded	1.737
r_angle_refined_deg	1.644
r_mcbond_it	1.044
r_nbtor_refined	0.334
r_nbd_refined	0.279
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3121
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	47

Software

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