1TNB | pdb_00001tnb

Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a substrate KKSKTKCVIF Peptide Derived from TC21

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N4Q	pdb entry 1N4Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	291	1.3 M ammonium sulfate, 175 mM NaCitrate pH 6.5, 100 mM MES pH 6.3, 20 mM DTT, 1uM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
5.5	77.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 271.13	α = 90
b = 266.72	β = 131.68
c = 185.141	γ = 90

Symmetry
Space Group	C 1 2 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	Bent cylindrical Si-mirror (Rh coating)	2002-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9000	APS	14-BM-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.85	30	95.6	0.077	11.1	2.9	227549	217761	-0.5	-0.5	39.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.85	2.95	88.8		0.277	2.7		20145

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1N4Q	2.85	27.66	-0.5	227773	213442	10796	93.6	0.189	0.189	0.189	0.18	0.21	0.2	RANDOM	46.7

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]
-4.87		-4.3	11.19		-6.31

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.8
c_scangle_it	3.18
c_mcangle_it	2.11
c_scbond_it	2.02
c_mcbond_it	1.23
c_angle_deg	1.2
c_improper_angle_d	0.78
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32428
Nucleic Acid Atoms
Solvent Atoms	881
Heterogen Atoms	195

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.