1U18

1.96 A Crystal structure of H60C mutant of nitrophorin complexed with histamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NP1	PDB Entry 2NP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1 M potassium cacodylate, 2.9 M di-ammonium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.82	α = 90
b = 73.85	β = 98.57
c = 65.38	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 confocal mirrors	2003-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	1.96	27	92	0.038	11.2	2.1	26246	22695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.96	2.06	70.4		0.038	0.0125	3.4	1.08	3724

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 2NP1	1.96	27	22659	22659	1192	90.75	0.18703	0.18703	0.18498	0.22562	RANDOM	33.658

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]
-0.27		-2.7	-0.12		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.151
r_dihedral_angle_1_deg	5.745
r_scbond_it	4.217
r_mcangle_it	2.871
r_angle_refined_deg	1.997
r_mcbond_it	1.729
r_angle_other_deg	0.991
r_symmetry_vdw_other	0.33
r_nbd_other	0.262
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.206
r_chiral_restr	0.163
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.136
r_nbtor_other	0.092
r_bond_refined_d	0.032
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2878
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	112

Software

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