2GBR

Crystal Structure of the 35-36 MoaD 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	3.9	293.15	24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.465	α = 90
b = 54.807	β = 90
c = 92.627	γ = 90

Symmetry
Space Group	P 21 21 21

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	2	5	99.4	0.135	5.9	3.86	14781	14696

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)
	2	2.07	100	100	0.421	2.5	3.9	1447

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	2	4.99	14781	14668	745	99.26	0.21938	0.21938	0.21583	0.23	0.28971	0.3	RANDOM	22.689

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]
-0.02			0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.294
r_dihedral_angle_3_deg	15.577
r_dihedral_angle_4_deg	15.311
r_dihedral_angle_1_deg	5.667
r_scangle_it	2.746
r_scbond_it	1.775
r_angle_refined_deg	1.237
r_mcangle_it	0.965
r_mcbond_it	0.838
r_angle_other_deg	0.795
r_symmetry_metal_ion_refined	0.493
r_symmetry_vdw_refined	0.442
r_xyhbond_nbd_refined	0.256
r_metal_ion_refined	0.243
r_symmetry_hbond_refined	0.243
r_nbd_refined	0.213
r_symmetry_vdw_other	0.202
r_nbd_other	0.179
r_nbtor_refined	0.168
r_mcbond_other	0.142
r_nbtor_other	0.083
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1840
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	13

Software

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