2J5Q

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O6Z	PDB ENTRY 1O6Z

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
3.42	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.976	α = 90
b = 114.32	β = 93.47
c = 124.117	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	2.15	20	95.5	0.1	11.4	3.3		91779			11.88

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	2.15	2.27	89.2		0.28	3.4	3.1

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	2.15	20	91779	4588	95.5	0.2196	0.2196	0.267	RANDOM	22

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]
-7.981		0.006	1.428		6.553

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.36
c_scangle_it	4.237
c_scbond_it	3.204
c_mcangle_it	2.818
c_mcbond_it	2.027
c_angle_deg	1.49125
c_improper_angle_d	0.94
c_bond_d	0.011226
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