2GBN

Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GBM	PDB ENTRY 2GBM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	279.15	25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.773	α = 90
b = 45.773	β = 90
c = 111.549	γ = 120

Symmetry
Space Group	P 65 2 2

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		2005-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00808	APS	17-ID

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	1.6	37.35	100	0.094	16.5	19.17	9821	9821

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	100	100	0.654	3.8	14.02

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2GBM	1.6	37.35	9821	9768	469	99.96	0.20591	0.20591	0.20298	0.21	0.26491	0.28	RANDOM	20.801

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]
0.93	0.47		0.93		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.081
r_dihedral_angle_4_deg	16.802
r_dihedral_angle_3_deg	15.17
r_dihedral_angle_1_deg	6.517
r_scangle_it	5.992
r_scbond_it	5.035
r_sphericity_bonded	4.217
r_rigid_bond_restr	4.046
r_mcangle_it	2.798
r_mcbond_it	2.192
r_angle_refined_deg	1.947
r_angle_other_deg	1.036
r_mcbond_other	0.617
r_nbd_refined	0.25
r_symmetry_vdw_other	0.248
r_symmetry_hbond_refined	0.244
r_nbd_other	0.202
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.188
r_chiral_restr	0.126
r_nbtor_other	0.089
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	620
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction