1J2R | pdb_00001j2r

Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NBA	PDB entries 1NBA and 1IM5
experimental model	PDB	1IM5	PDB entries 1NBA and 1IM5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5.5	293	MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.502	α = 90
b = 108.886	β = 90
c = 50.419	γ = 90

Symmetry
Space Group	P 21 21 2

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		2002-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	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	1.3	50.77	85.9	0.059	6.4	5.5	190258	163406		3	18.62

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	1.3	1.35	72.6		0.064		2.5	13256

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 (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 entries 1NBA and 1IM5	1.3	50.77	162173	155206	8200	85.89	0.14596	0.14499	0.15	0.16494	0.17	RANDOM	11.354

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]
-0.5			-0.03		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.611
r_scangle_it	3.092
r_scbond_it	1.926
r_angle_refined_deg	1.399
r_mcangle_it	1.263
r_angle_other_deg	0.83
r_mcbond_it	0.691
r_symmetry_vdw_other	0.271
r_nbd_other	0.253
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.083
r_nbtor_other	0.083
r_gen_planes_other	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
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	5751
Nucleic Acid Atoms
Solvent Atoms	924
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
TRUNCATE	data scaling
T-COFFEE	phasing
MODELLER	phasing
AMoRE	phasing