2GRF | pdb_00002grf

Crystal structure of Scapharca inaequivalvis HBI, M37V mutant in the absence of ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4SDH	4SDH (DEOXY WILD TYPE HBI)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	8.5	298	PHOSPHATE BUFFER, pH 8.50, SMALL TUBES, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.74	α = 90
b = 44.51	β = 90
c = 144.05	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 IIC	YALE MIRRORS	2000-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	40	90.9	0.089	9.3	2.9	17677	16213		1	12.5

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)
	2.1	2.18	86.7		0.311			1503

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-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	4SDH (DEOXY WILD TYPE HBI)	2.1	30.75	17677	16104	782	91.1	0.204	0.184	0.184	0.18	0.229	0.22	RANDOM	20.7

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]
-1.58			-3.75		5.32

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.3
c_scangle_it	6.39
c_scbond_it	5.05
c_mcangle_it	3.48
c_mcbond_it	2.89
c_improper_angle_d	1.12
c_angle_deg	1.1
c_bond_d	0.005
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	2230
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	86

Software

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