3RWO

Crystal structure of YPT32 in complex with GDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 4000, MGCL2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130	α = 90
b = 45.2	β = 110.5
c = 73.4	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	MARMOSAIC 225 mm CCD		2009-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.7	68.75	99.4	0.052				44104		-3	24.66

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	1.7	1.75	98.9		0.401	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CPJ	1.7	68.75	44104	2223	99.5	0.169	0.167	0.203	RANDOM	20.173

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]
-0.37		-0.08	0.15		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.159
r_dihedral_angle_4_deg	18.007
r_dihedral_angle_3_deg	14.316
r_dihedral_angle_1_deg	5.753
r_scangle_it	3.029
r_scbond_it	1.944
r_mcangle_it	1.418
r_angle_refined_deg	1.333
r_mcbond_it	0.778
r_chiral_restr	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2700
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	58

Software

Software
Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling