1QYA

CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20% PEG 600, 0.1 M IMIDAZOLE-MALATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.159	α = 90
b = 79.631	β = 115.26
c = 77.022	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		2002-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9330,0.9340	ESRF	ID14-1

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	20	94.6	0.044	12	2.7		49349

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	2	2.05	94.6		0.431	1.7	2.6

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	YDDE SOLVED BY SAD ON SE-MET EDGE	2	20	44289	2407	94.07	0.18838	0.18626	0.22761	RANDOM

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]
0.28		-1.69	1.21		-2.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.117
r_scangle_it	2.453
r_scbond_it	1.457
r_angle_refined_deg	1.201
r_mcangle_it	0.953
r_angle_other_deg	0.767
r_mcbond_it	0.52
r_symmetry_vdw_other	0.271
r_nbd_other	0.237
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.082
r_nbtor_other	0.08
r_chiral_restr	0.073
r_symmetry_hbond_refined	0.058
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4610
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling