1Y21 | pdb_00001y21

Crystal Structure of Cimex Nitrophorin 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	PDB entry 1NTF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	298	PEG 4000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.84	32.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.065	α = 90
b = 41.477	β = 94.55
c = 65.346	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	IMAGE PLATE	RIGAKU RAXIS IV	osmic mirrors	2002-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	1.75	64.55	98.7	0.043	20	3.3	24549	24549			24.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	98.4		0.24	2.6	2.7	6875

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	PDB entry 1NTF	1.75	64.55	24549	24549	1255	98.54	0.1696	0.1696	0.16766	0.18	0.20828	0.18	RANDOM	27.019

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]
-0.11		-0.97	0.05		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.833
r_scangle_it	4.885
r_scbond_it	3.093
r_mcangle_it	2.386
r_angle_refined_deg	1.831
r_mcbond_it	1.383
r_angle_other_deg	0.912
r_nbd_other	0.251
r_nbd_refined	0.219
r_symmetry_vdw_other	0.205
r_xyhbond_nbd_refined	0.187
r_symmetry_hbond_refined	0.168
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.116
r_nbtor_other	0.087
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	55

Software

Software
Software Name	Purpose
CrystalClear	data collection
d*TREK	data reduction
MLPHARE	phasing
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling