2J5R

2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (radiation damage series)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7		3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
3.45	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.377	α = 90
b = 114.574	β = 93.34
c = 124.529	γ = 90

Symmetry
Space Group	C 1 2 1

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 CCD	MIRRORS	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.25	20	96.2	0.11	11.1	3.3		81346			15.716

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	2.25	2.37	90.8		0.33	3	3.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1O6Z	2.25	20	81346	4084	96.1	0.2199	0.2199	0.271	RANDOM	24.3193

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]
-9.1		-0.194	1.712		7.388

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.31
c_scangle_it	4.367
c_scbond_it	3.205
c_mcangle_it	2.826
c_mcbond_it	1.958
c_angle_deg	1.43407
c_improper_angle_d	0.92
c_bond_d	0.01013
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	9051
Nucleic Acid Atoms
Solvent Atoms	1023
Heterogen Atoms	8

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling