1NZJ

Crystal Structure and Activity Studies of Escherichia Coli Yadb ORF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GLN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	PEG4000, MPD, Nacacodylate, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.92	α = 90
b = 39.3	β = 116.19
c = 69.15	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		2002-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		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	1.5	62.02	99.4	0.057	9.1	3.7		43648

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)
	1.5	1.58	99.4		0.283	2.5	3.5

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-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GLN	1.5	24.254	40227	40227	3063	96	0.1472	0.14729	0.14559	0.17	0.16969	RANDOM	12.591

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]
-0.99		-1.04	-0.07		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	7.6
r_dihedral_angle_1_deg	5.145
r_scangle_it	3.699
r_scbond_it	2.426
r_sphericity_bonded	2.376
r_mcangle_it	1.601
r_angle_refined_deg	1.204
r_mcbond_it	0.967
r_angle_other_deg	0.835
r_rigid_bond_restr	0.618
r_symmetry_vdw_other	0.288
r_symmetry_vdw_refined	0.284
r_nbd_other	0.237
r_symmetry_hbond_refined	0.228
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.08
r_nbtor_other	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	1

Software

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