Experiment: 1JML

Conversion of Monomeric Protein L to an Obligate Dimer by Computational Protein Design

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HZ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	175mM Zinc Acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.762	α = 90
b = 76.744	β = 90
c = 59.797	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IV	Mirrors	2000-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	30	99.7	0.064	0.076	16.6	4.5	8795	8777	-3	-3	15.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	99.3		0.17	0.172	7.8	7.2	589

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1hz5	1.9	23.59	8795	8777	873	99.7	0.193	0.1927	0.218	0.2182	RANDOM	29.3

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]
2.89			-0.07		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.7
c_scangle_it	4.7
c_scbond_it	3.24
c_mcangle_it	2.19
c_mcbond_it	1.42
c_angle_deg	1.4
c_improper_angle_d	0.72
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	559
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	3

Software

Software
Software Name	Purpose
EPMR	phasing
CNS	refinement
SCALEPACK	data scaling