4L20 | pdb_00004l20

Crystal structure of Cimex nitrophorin A21V mutant ferrous NO complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.963	α = 90
b = 41.814	β = 94.91
c = 65.241	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	bent (Si)-mirror	2008-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9798	SSRL	BL9-2

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	1.68	40.73	99.8	0.055	13.6	5.24	158351	30208			32.8

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	1.68	1.74	100		0.277	4.2	5.2	3023

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	FOURIER SYNTHESIS	THROUGHOUT	1NTF	1.68	35.16	158351	28675	1528	99.74	0.17798	0.17798	0.1756	0.1861	0.22145	0.2314	RANDOM	27.284

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]
0.05		-0.2	-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.91
r_dihedral_angle_4_deg	15.932
r_dihedral_angle_3_deg	14.572
r_dihedral_angle_1_deg	6.97
r_angle_refined_deg	1.933
r_angle_other_deg	0.939
r_chiral_restr	0.124
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2231
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	45

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
REFMAC	phasing