1Z9T | pdb_00001z9t

CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI AT 1.54 A RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U05

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5	277	0.2M (NH4)2HCitrate, 20.0% PEG-3350, No Buffer pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	49.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.711	α = 90
b = 80.711	β = 90
c = 90.589	γ = 90

Symmetry
Space Group	P 43 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 315	Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)	2005-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.54	60.3	100	0.079	6.7	6.8		44917

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.58		100	0.758	1	7

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 (All)	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	1u05	1.54	60.3	42591	2262	99.95	0.143	0.14324	0.142	0.16	0.172	0.19	RANDOM	17.354

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]
-0.57			-0.57		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.249
r_dihedral_angle_4_deg	17.24
r_dihedral_angle_3_deg	11.755
r_scangle_it	6.193
r_dihedral_angle_1_deg	5.88
r_scbond_it	4.358
r_mcangle_it	2.437
r_mcbond_it	2.004
r_angle_refined_deg	1.732
r_angle_other_deg	1.447
r_mcbond_other	0.474
r_symmetry_vdw_other	0.238
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.211
r_nbd_other	0.189
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.142
r_chiral_restr	0.098
r_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1799
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing