1I24 | pdb_00001i24

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD-TYPE PROTEIN SQD1, WITH NAD AND UDP-GLUCOSE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	ammonium sulfate, sodium chloride, MES buffer, NAD+, UDP-glucose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.5	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.243	α = 90
b = 160.243	β = 90
c = 99.273	γ = 90

Symmetry
Space Group	I 41 2 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	CUSTOM-MADE		1999-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	1.14	99	86.4	0.097	21.4	5.9		196326		-3	11.59

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	1.14	1.19	38		0.366	1.7	1.4

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	PDB ENTRY 1QRR	1.2	20	184009	9260	92.3	0.192	0.192	0.1822	0.198	0.1883	REFLECTIONS FOR CROSS-VALIDATION WERE SELECTED FROM A STANDARD SET OF DUMMY DATA GENERATED USING THE CCP4 SUITE, WHERE 5% OF THE RELECTIONS ARE FLAGGED. THE SELECTED REFLECTIONS MATCH THOSE IN PDB ENTRY 1QRR.	13.43

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.74
c_scangle_it	1.983
c_angle_deg	1.58
c_scbond_it	1.361
c_mcangle_it	1.117
c_improper_angle_d	1.11
c_mcbond_it	0.798
c_bond_d	0.012
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3032
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	90

Software

Software
Software Name	Purpose
d*TREK	data scaling
HKL-2000	data collection
SCALEPACK	data scaling
TRUNCATE	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
CCP4	data scaling
CNS	phasing