1PB3 | pdb_00001pb3

Sites of binding and orientation in a four location model for protein stereospecificity.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	295	IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.669	α = 90
b = 103.669	β = 90
c = 150.124	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 4		1999-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.000	ALS	5.0.2

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	1.7	25	97.8	0.068	32	19	90369	88368			20.5

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	1.7	1.76	100		0.5	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	24.93	90369	88368	8832	97.8	0.194	0.194	0.194	0.216	RANDOM	24.6

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]
1.29			1.29		-2.58

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.2
c_scangle_it	4.28
c_scbond_it	2.75
c_mcangle_it	2.18
c_angle_deg	1.6
c_mcbond_it	1.38
c_improper_angle_d	0.99
c_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3213
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	28

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing