2GBJ | pdb_00002gbj

Crystal Structure of the 9-10 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	1UBQ	PDB ENTRY 1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	279.15	27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

Crystal Properties
Matthews coefficient	Solvent content
1.736554	29.170057

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.124	α = 90
b = 53.035	β = 90
c = 87.268	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	NOIR-1	180 cm lens focused ccd	2004-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.12711	ALS	4.2.2

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	1.35	33.691	97.8	0.068	10.8	4.98	28499	27867

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)
	1.35	1.4	90.6	90.6	0.503	2.4	4.37	2511

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 1UBQ	1.35	33.691	28499	27864	1405	97.78	0.18998	0.18998	0.18805	0.34	0.22589	0.37	RANDOM	33.353

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]
			-0.59		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.53
r_dihedral_angle_4_deg	20.878
r_dihedral_angle_3_deg	13.379
r_dihedral_angle_1_deg	6.042
r_scangle_it	4.494
r_scbond_it	3.215
r_sphericity_bonded	2.737
r_mcangle_it	1.946
r_rigid_bond_restr	1.921
r_mcbond_it	1.657
r_angle_refined_deg	1.416
r_angle_other_deg	0.86
r_mcbond_other	0.646
r_symmetry_vdw_other	0.243
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.206
r_nbd_other	0.188
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.083
r_nbtor_other	0.08
r_xyhbond_nbd_other	0.04
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1259
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms

Software

Software
Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection