3RIP | pdb_00003rip

Crystal Structure of human gamma-tubulin complex protein 4 (GCP4)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		THE STARTING MODEL WAS SOLVED AND PARTIALLY REFINED FROM SAD DATA COLLECTED USING THE SELENEMETHIONINE PROTEIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	285	8-10% MPD (2-methyl-2,4-pentanediol), 0-20% glycerol (w/v), 300-400 mM Tris-Hcl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
5.56	77.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.95	α = 90
b = 214.95	β = 90
c = 128.66	γ = 120

Symmetry
Space Group	P 63 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 315r		2009-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.033	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	20	99.4		5.4	77508	73248	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.4	99.9		2.45		9151

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	THE STARTING MODEL WAS SOLVED AND PARTIALLY REFINED FROM SAD DATA COLLECTED USING THE SELENEMETHIONINE PROTEIN	2.3	20	77508	73248	3848	99.47	0.228	0.22837	0.22671	0.25992	0.236	RANDOM	52.981

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]
1.92	0.96		1.92		-2.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.004
r_dihedral_angle_4_deg	21.073
r_dihedral_angle_3_deg	19.268
r_dihedral_angle_1_deg	6.252
r_scangle_it	5.046
r_scbond_it	3.148
r_mcangle_it	2.645
r_angle_refined_deg	2.105
r_mcbond_it	1.784
r_chiral_restr	0.131
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4540
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	56

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling