2GBK | pdb_00002gbk

Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	293.15	27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.046	α = 79.91
b = 45.895	β = 74.99
c = 54.382	γ = 81.33

Symmetry
Space Group	P 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				2004-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	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	1.99	5.8	90.7	0.084	9.6	2.73	18012	16333

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	1.99	2.06	89.8	89.8	0.157	4.2	2.66	1603

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 2GBJ	1.99	5.8	18012	16331	850	90.73	0.24638	0.24638	0.24403	0.25	0.28668	0.29	RANDOM	18.166

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]
0.95	1.32	-1.08	-1.48	0.29	0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.735
r_dihedral_angle_4_deg	12.801
r_dihedral_angle_3_deg	12.476
r_dihedral_angle_1_deg	5.022
r_angle_refined_deg	0.857
r_angle_other_deg	0.743
r_scangle_it	0.733
r_scbond_it	0.479
r_mcangle_it	0.263
r_mcbond_it	0.233
r_nbd_other	0.163
r_nbd_refined	0.157
r_symmetry_vdw_other	0.152
r_nbtor_refined	0.151
r_symmetry_hbond_refined	0.139
r_symmetry_vdw_refined	0.118
r_xyhbond_nbd_refined	0.086
r_nbtor_other	0.075
r_chiral_restr	0.05
r_mcbond_other	0.034
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2597
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms

Software

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