Experiment: 1V9N

Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.1	295	PEG, HEPES, LiCl2, pH 5.1, MICROBATCH, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.52	50.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.19	α = 90
b = 74.19	β = 90
c = 127.28	γ = 120

Symmetry
Space Group	P 31 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	IMAGE PLATE	RIGAKU RAXIS		2003-11-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.985, 0.97914, 0.97944	SPring-8	BL26B1

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	2.1	30	99.7	0.073		5.9	24361	24293			14.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.23	100

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	28.68	24361	24293	1168	99.9	0.208	0.208	0.2082	0.243	0.243	RANDOM	30.5

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]
3.68	2.01		3.68		-7.36

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.8
c_angle_deg	1.3
c_improper_angle_d	0.76
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2617
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	54

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing