4YNX | pdb_00004ynx

Structure of YdiE from E. coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JRA	MOLECULAR DYNAMICS SIMULATION OF PDB 2JRA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	1.6 M ammonium sulphate, 0.1M Tris

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.736	α = 90
b = 38.189	β = 90
c = 54.728	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	ADSC QUANTUM 210		2003-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.900	SPring-8	BL38B1

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	1.497	30.5	98.4	0.063	19.3	4.4		12710

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)
	1.497	1.554	95.8		0.346	4.1	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MOLECULAR DYNAMICS SIMULATION OF PDB 2JRA	1.5	30.5	12085	623	100	0.175	0.1712	0.1705	0.2502	0.2521	RANDOM	16.45

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]
-0.76			0.05		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.309
r_dihedral_angle_4_deg	19.59
r_dihedral_angle_3_deg	14.052
r_scangle_it	8.666
r_dihedral_angle_1_deg	6.436
r_scbond_it	5.693
r_mcangle_it	3.814
r_rigid_bond_restr	2.664
r_mcbond_it	2.488
r_angle_refined_deg	2.028
r_chiral_restr	0.139
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	648
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction