2QFZ | pdb_00002qfz

Crystal structure of human TBC1 domain family member 22A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G77	PDB entry 2G77

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	28.0% PEG400, 0.2M Calcium chloride, 0.1M Sodium HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.911	α = 90
b = 121.515	β = 93.64
c = 66.278	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 4		2007-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	1.1000	NSLS	X12B

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	2.1	30	100	0.152	6.5	6.4		39313

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)
	2.1	2.18		100	0.966		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 2G77	2.1	30	39184	2049	99.187	0.205	0.2021	0.21	0.2571	0.26	thin shells	25.763

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]
0.597		-1.056	-0.924		0.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.673
r_dihedral_angle_4_deg	18.829
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	5.574
r_mcangle_it	3.883
r_scangle_it	3.786
r_scbond_it	2.776
r_mcbond_it	2.742
r_angle_refined_deg	1.395
r_angle_other_deg	0.993
r_mcbond_other	0.77
r_nbd_refined	0.206
r_nbd_other	0.185
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.155
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_other	0.14
r_nbtor_other	0.087
r_chiral_restr	0.083
r_bond_refined_d	0.017
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	4900
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection