1M5U | pdb_00001m5u

CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH 8.0 IN THE APO-FORM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		APO-DIVK SOLVED AT PH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING OR SITTING-DROP	8	285	MES 50mM PH6.0,PEG MME 550 32% At 285K. The Protein was Concentrated At 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing PEG MME 550 (32%), MES PH 6.00 (40 mM), DTT (5mM). Crystal Size (300X40X40 microM3) In 20microL Sitting Drops. VAPOR DIFFUSION, HANGING OR SITTING-DROP at 285K. Crystals Were Transferred In Reservoir Solutions Whose Ph Was Increased From 6.0 To 8.0 By Steps Of 0.5 Ph Units (The Soaking Time In Each Solution Was 12 Hours). Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In Peg Mme 550 (50%), Tris Ph 8.0 (40 Mm)., pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
1.8	31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.67	α = 90
b = 40.71	β = 90
c = 66.29	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	100	IMAGE PLATE	MARRESEARCH		2000-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.980	ESRF	BM30A

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	1.87	35	97.9	0.037	11.3	5.1	8414	8414			16.4

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)
	1.87	1.97	94.1		0.097	7.9	4.4	5050

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	APO-DIVK SOLVED AT PH6	1.87	15	3	8414	8022	854	93.4	0.1901	0.1901	0.19	0.2026	0.206	0.2145	RANDOM	22.7

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]
-0.08			1.45		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.6
c_scangle_it	2.41
c_mcangle_it	1.78
c_scbond_it	1.64
c_angle_deg	1.3
c_mcbond_it	1.16
c_improper_angle_d	0.71
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	895
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing